NAR Web Server Issue (July 1, 2004)
Source: http://nar.oupjournals.org/content/vol32/suppl_2/
Total Links: 145
3DCoffee
Sequence Comparison >
Multiple Sequence Alignments
Multiple sequence alignment program which uses both sequence and structural information to construct alignments.
Multiple sequence alignment program which uses both sequence and structural information to construct alignments.
ACMES
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences
ACMES (Advanced Content Matching Engine for Sequences) is a server that can be used to search for short repeats (between 3 and 10 000 bases) across multiple species. Users can limit results of a search by keyword searches.
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences
ACMES (Advanced Content Matching Engine for Sequences) is a server that can be used to search for short repeats (between 3 and 10 000 bases) across multiple species. Users can limit results of a search by keyword searches.
ADVICE
Protein >
Interactions, Pathways, Enzymes
Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested that co-evolution of proteins is useful for predicting and validating protein-protein interactions.
Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested that co-evolution of proteins is useful for predicting and validating protein-protein interactions.
AGenDA
DNA >
Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences
AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.
Sequence Comparison > Analysis of Aligned Sequences
AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.
ArrayPipe
Expression >
Transcript Expression & Microarrays
ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.
ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.
ArrayProspector
Expression >
Transcript Expression & Microarrays
ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.
ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.
ArrayXPath
Expression >
Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.
Protein > Interactions, Pathways, Enzymes
ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.
ASmodeler
Expression >
Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences
Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences
Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.
AUGUSTUS
DNA >
Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs
AUGUSTUS is a eukaryotic gene prediction tool for modeling intron length distribution, and searching for motifs and multiple splice variants. It is particularly effective with larger sequences. It can be run through a web interface, or downloaded and run locally.
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs
AUGUSTUS is a eukaryotic gene prediction tool for modeling intron length distribution, and searching for motifs and multiple splice variants. It is particularly effective with larger sequences. It can be run through a web interface, or downloaded and run locally.
BEARR
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Human Genome > Other Resources
Model Organisms > Mouse and Rat
Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3' terminus to look for the patterns.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Human Genome > Other Resources
Model Organisms > Mouse and Rat
Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3' terminus to look for the patterns.
BioInfo3D
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.
BioProspector
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.
BLAST
DNA >
Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching
Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching
Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
BLAST Filter
Sequence Comparison >
Similarity Searching
A tool that uses BLAST analyses to assemble a set of sequences from a single query sequence. Users can customize rules which act to filter out certain sequences from the full set of BLAST results.
A tool that uses BLAST analyses to assemble a set of sequences from a single query sequence. Users can customize rules which act to filter out certain sequences from the full set of BLAST results.
BOMP
Protein >
2-D Structure Prediction
Protein > Localization and Targeting
The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.
Protein > Localization and Targeting
The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.
BSDD
Protein >
3-D Structural Features
Protein > 3-D Structure Retrieval, Viewing
BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.
Protein > 3-D Structure Retrieval, Viewing
BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.
CARNAC
RNA >
Structure Prediction, Visualization, and Design
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.
CARRIE
Expression >
Gene Regulation
Expression > Transcript Expression & Microarrays
Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.
Expression > Transcript Expression & Microarrays
Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.
CaspR
Protein >
3-D Structure Prediction
CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.
CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.
CD-Search
Protein >
3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.
Protein > Domains and Motifs
CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.
CE-MC
Protein >
3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments
A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.
Sequence Comparison > Multiple Sequence Alignments
A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.
CHAOS/DIALIGN WWW server
Sequence Comparison >
Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments
The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.
Sequence Comparison > Multiple Sequence Alignments
The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.
CHOP
DNA >
Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences
The coding-region hunting online program (CHOP) compares two nucleotide sequences, and plots three measures of conservation between them by extracting and grouping every third residue in 60bp units of aligned data. This allows the visualization of the amount of 'wobble' present, which can be used to identify potential coding regions.
Sequence Comparison > Analysis of Aligned Sequences
The coding-region hunting online program (CHOP) compares two nucleotide sequences, and plots three measures of conservation between them by extracting and grouping every third residue in 60bp units of aligned data. This allows the visualization of the amount of 'wobble' present, which can be used to identify potential coding regions.
CHOP
Protein >
Domains and Motifs
Sequence Comparison > Similarity Searching
CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.
Sequence Comparison > Similarity Searching
CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.
ClusPro
Protein >
Molecular Dynamics and Docking
ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.
ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.
COLORADO-3D
Protein >
3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval, Viewing
COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval, Viewing
COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.
CompareProspector
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.
CONFAC
Expression >
Gene Regulation
Expression > Transcript Expression & Microarrays
The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.
Expression > Transcript Expression & Microarrays
The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.
ConPred II
Protein >
2-D Structure Prediction
Protein > Localization and Targeting
ConPred II is a tool for predicting transmembrane topology for a user-supplied query sequence. Results are presented in a variety of forms including hydropathy plots.
Protein > Localization and Targeting
ConPred II is a tool for predicting transmembrane topology for a user-supplied query sequence. Results are presented in a variety of forms including hydropathy plots.
Consensus Server
Protein >
3-D Structure Comparison
The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling.
The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling.
Consite
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.
Expression > Gene Regulation
Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.
CRASP
Sequence Comparison >
Analysis of Aligned Sequences
Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.
Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.
CREME
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources
CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.
Expression > Gene Regulation
Human Genome > Other Resources
CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.
CSTminer
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences
CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences
CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.
CVTree
Model Organisms >
Microbes
Protein > Phylogeny Reconstruction
Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.
Protein > Phylogeny Reconstruction
Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.
CysView
Protein >
Biochemical Features
Protein > Sequence Features
CysView takes as input various annotated formats of protein sequences, and graphically displays cysteine pairing patterns. It also groups proteins with similar disulfide connectivity patterns.
Protein > Sequence Features
CysView takes as input various annotated formats of protein sequences, and graphically displays cysteine pairing patterns. It also groups proteins with similar disulfide connectivity patterns.
DEQOR
DNA >
Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.
DIALIGN
Sequence Comparison >
Multiple Sequence Alignments
Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.
Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.
DICHROWEB
Protein >
2-D Structure Prediction
A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.
A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.
DTFAM
Human Genome >
Health and Disease
Literature > Text Mining
Protein > Annotation and Function
Dragon TF Association Miner (DTFAM) is text-mining tool which takes Pubmed abstracts/summaries as input and reports potential associations between transcription factors and diseases/GO ontologies. The user can also provide a PubMed query directly to DTFAM and its output will be analysed when the search has completed. There is a limit of 5000 abstracts per session.
Literature > Text Mining
Protein > Annotation and Function
Dragon TF Association Miner (DTFAM) is text-mining tool which takes Pubmed abstracts/summaries as input and reports potential associations between transcription factors and diseases/GO ontologies. The user can also provide a PubMed query directly to DTFAM and its output will be analysed when the search has completed. There is a limit of 5000 abstracts per session.
E2G
Expression >
cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools
E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.
Sequence Comparison > Other Alignment Tools
E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.
EBI Public Web-Services
Education >
Directories and Portals
The European Bioinformatics Institute (EBI) Services page is a portal to various public access databases and tools for information retrieval, analysis, and data submission provided by the EBI. The services include access to sequence, literature, microarray, and structure databases, and to tools such as BLAST, ClustalW, DALI, and InterProScan for sequence, structural and functional analysis. Various databases and software tools are also downloadable via FTP.
The European Bioinformatics Institute (EBI) Services page is a portal to various public access databases and tools for information retrieval, analysis, and data submission provided by the EBI. The services include access to sequence, literature, microarray, and structure databases, and to tools such as BLAST, ClustalW, DALI, and InterProScan for sequence, structural and functional analysis. Various databases and software tools are also downloadable via FTP.
ECR Browser
Model Organisms >
Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences
The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences
The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.
Electronic PCR
DNA >
Tools For the Bench
Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.
Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.
ElNemo
Protein >
3-D Structure Retrieval, Viewing
Protein > Molecular Dynamics and Docking
ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.
Protein > Molecular Dynamics and Docking
ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.
ERPIN
RNA >
Motifs
RNA > Structure Prediction, Visualization, and Design
ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.
RNA > Structure Prediction, Visualization, and Design
ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.
ESLpred
Protein >
Localization and Targeting
ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.
ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.
Expression Profiler
Expression >
Transcript Expression & Microarrays
Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.
Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.
FAN
DNA >
Annotations
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Annotation and Function
Protein > Domains and Motifs
FAN (Fingerprint Analysis of Nucleotide sequences) searches nucleotide sequences against the PRINTS database, a collection of protein fingerprints used to assign uncharacterized sequences to known families and hence to infer tentative functions.
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Annotation and Function
Protein > Domains and Motifs
FAN (Fingerprint Analysis of Nucleotide sequences) searches nucleotide sequences against the PRINTS database, a collection of protein fingerprints used to assign uncharacterized sequences to known families and hence to infer tentative functions.
FATCAT
Protein >
3-D Structure Comparison
FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT) algorithm.
FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT) algorithm.
FoldMiner and LOCK 2
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.
GDAP
Protein >
Biochemical Features
Protein > Sequence Features
The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.
Protein > Sequence Features
The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.
Gene2Oligo
DNA >
Tools For the Bench
Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).
Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).
Genotyping - NCBI
Model Organisms >
Other Organisms
Sequence Comparison > Other Alignment Tools
The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.
Sequence Comparison > Other Alignment Tools
The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.
GEPAS
DNA >
Sequence Polymorphisms
Expression > Transcript Expression & Microarrays
The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.
Expression > Transcript Expression & Microarrays
The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.
GFINDer
Expression >
Transcript Expression & Microarrays
Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.
Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.
GlycoFragment
Other Molecules >
Carbohydrates
GlycoFragment is a tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra.
GlycoFragment is a tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra.
GlycoSearchMS
Other Molecules >
Carbohydrates
GlycoSearchMS takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures.
GlycoSearchMS takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures.
GOAL
Expression >
cDNA, EST, SAGE
Expression > Transcript Expression & Microarrays
Gene Ontology Automated Lexicon (GOAL) is a tool for the functional analysis of data from SAGE and microarray experiments. Gene Ontology terms are used as the basis for statistical analysis.
Expression > Transcript Expression & Microarrays
Gene Ontology Automated Lexicon (GOAL) is a tool for the functional analysis of data from SAGE and microarray experiments. Gene Ontology terms are used as the basis for statistical analysis.
GOblet
Protein >
Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences
GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.
Sequence Comparison > Analysis of Aligned Sequences
GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.
GPCRpred
Protein >
Annotation and Function
GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.
GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.
GraphAlign
Sequence Comparison >
Alignment Editing and Visualization
Provides graphical representations of ClustalW global pairwise alignments for query and subject sequences from BLAST type searches. Graphical representation provides information on high quality sections of the global alignment.
Provides graphical representations of ClustalW global pairwise alignments for query and subject sequences from BLAST type searches. Graphical representation provides information on high quality sections of the global alignment.
IBM Bioinformatics and Pattern Discovery Group
DNA >
Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments
Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments
Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.
IBM Genome Annotation Page
DNA >
Annotations
Human Genome > Annotations
Model Organisms > Fish
Model Organisms > Fly
Model Organisms > General Resources
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Other Organisms
Model Organisms > Worm
Model Organisms > Yeast
Protein > Phylogeny Reconstruction
Sequence Comparison > Comparative Genomics
IBM's Bio-Dictionary-based Annotations Of Completed Genomes page lists annotations for over 75 complete genomes (archae, bacteria, eurkaryotes, and viruses). You can query these annotations at the sequence level as well as search/compare across genomes.
Human Genome > Annotations
Model Organisms > Fish
Model Organisms > Fly
Model Organisms > General Resources
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Other Organisms
Model Organisms > Worm
Model Organisms > Yeast
Protein > Phylogeny Reconstruction
Sequence Comparison > Comparative Genomics
IBM's Bio-Dictionary-based Annotations Of Completed Genomes page lists annotations for over 75 complete genomes (archae, bacteria, eurkaryotes, and viruses). You can query these annotations at the sequence level as well as search/compare across genomes.
Iccare
Sequence Comparison >
Other Alignment Tools
The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.
The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.
ILM
RNA >
Structure Prediction, Visualization, and Design
Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.
Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.
IMGT/V-QUEST
Sequence Comparison >
Other Alignment Tools
The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.
The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.
iMolTalk
Protein >
2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
iMolTalk is a set of tools for protein structure analysis. Users have access to tools to extract information from PDB files, create Ramachandran plots or alpha-carbon distance matrices, align two structures or a sequence to a structure, search for contacts for a residue, and identify the interface between chains.
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
iMolTalk is a set of tools for protein structure analysis. Users have access to tools to extract information from PDB files, create Ramachandran plots or alpha-carbon distance matrices, align two structures or a sequence to a structure, search for contacts for a residue, and identify the interface between chains.
iMOT
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.
InterWeaver
Protein >
Interactions, Pathways, Enzymes
InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searches for interacting partners in protein interaction and literature databases, and the second finds sequence domains, and then searches for domain fusion events and possible domain interactions.
InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searches for interacting partners in protein interaction and literature databases, and the second finds sequence domains, and then searches for domain fusion events and possible domain interactions.
IsoFinder
DNA >
Structure and Sequence Feature Detection
IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.
IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.
ISOTOPICA
Protein >
Proteomics
Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.
Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.
JPD
Protein >
2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
Protein > Biochemical Features
Java Protein Dossier (JPD) is part of the STING Suite of web based programs for visualization and analyses of molecular structures. JPD can display many different physicochemical parameters for PDB files as well as for structurally aligned pairs of PDB files.
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
Protein > Biochemical Features
Java Protein Dossier (JPD) is part of the STING Suite of web based programs for visualization and analyses of molecular structures. JPD can display many different physicochemical parameters for PDB files as well as for structurally aligned pairs of PDB files.
KARMA
Expression >
Transcript Expression & Microarrays
KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.
KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.
KCaM
Protein >
Proteomics
The KEGG Carbohydrate Matcher (KCaM) takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm.
The KEGG Carbohydrate Matcher (KCaM) takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm.
LINKER
DNA >
Tools For the Bench
Protein > Biochemical Features
LINKER is a tool for designing linker peptide sequences for use in the construction of fusion proteins. The user provides the desired length of the linker in either Angstroms or number of residues, and several other constraints may also be specified, including the inclusion or exclusion of certain amino acids or protease sensitive sites.
Protein > Biochemical Features
LINKER is a tool for designing linker peptide sequences for use in the construction of fusion proteins. The user provides the desired length of the linker in either Angstroms or number of residues, and several other constraints may also be specified, including the inclusion or exclusion of certain amino acids or protease sensitive sites.
LOCtarget
Protein >
Annotation and Function
LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks.
LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks.
LowComplexity
DNA >
Structure and Sequence Feature Detection
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences
LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences
LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.
MAVL/StickWRLD
Sequence Comparison >
Analysis of Aligned Sequences
The Multiple Alignment Variation Linker (MAVL) examines a pre-aligned set of nucleotide or protein sequences and detects positive and negative interpositional correlations. The results can then be viewed as a StickWRLD representation.
The Multiple Alignment Variation Linker (MAVL) examines a pre-aligned set of nucleotide or protein sequences and detects positive and negative interpositional correlations. The results can then be viewed as a StickWRLD representation.
MDscan
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.
Meta-BASIC
Protein >
2-D Structure Prediction
Sequence Comparison > Similarity Searching
Meta-BASIC is a tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.
Sequence Comparison > Similarity Searching
Meta-BASIC is a tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.
MITOPRED
Protein >
Annotation and Function
MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.
MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.
MOLPROBITY
Protein >
3-D Structure Retrieval, Viewing
RNA > Structure Prediction, Visualization, and Design
MOLPROBITY is a structure validation program that can calculate and display steric, H-bonding, and van der Waals interactions for 3D structures of proteins, nucleic acids, and complexes.
RNA > Structure Prediction, Visualization, and Design
MOLPROBITY is a structure validation program that can calculate and display steric, H-bonding, and van der Waals interactions for 3D structures of proteins, nucleic acids, and complexes.
MONSTER
Protein >
3-D Structure Retrieval, Viewing
Protein > Biochemical Features
MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.
Protein > Biochemical Features
MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.
MotifViz
DNA >
Structure and Sequence Feature Detection
MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.
MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.
MoViES
DNA >
Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design
MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design
MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.
MSCAN
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
MSCAN takes as input one or more DNA sequences and a set of transcription factor binding site profiles. It then detects clusters of the binding sites in the sequences.
Expression > Gene Regulation
MSCAN takes as input one or more DNA sequences and a set of transcription factor binding site profiles. It then detects clusters of the binding sites in the sequences.
MyHits
Protein >
Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.
Sequence Comparison > Multiple Sequence Alignments
The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.
NLProt
Literature >
Text Mining
Protein > Sequence Retrieval
NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.
Protein > Sequence Retrieval
NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.
NRPS-PKS
Protein >
Domains and Motifs
NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.
NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.
Onto-Tools
DNA >
Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching
Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching
Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.
PathBLAST
Protein >
Interactions, Pathways, Enzymes
PathBLAST is a tool for cross-species comparison of protein interaction networks. PathBLAST takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the user.
PathBLAST is a tool for cross-species comparison of protein interaction networks. PathBLAST takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the user.
PDA
DNA >
Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Sequence Comparison > Analysis of Aligned Sequences
PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.
Human Genome > Sequence Polymorphisms
Sequence Comparison > Analysis of Aligned Sequences
PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.
PDB2PQR Server
Protein >
3-D Structural Features
Protein > Biochemical Features
Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.
Protein > Biochemical Features
Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.
PDBSiteScan
Protein >
3-D Structural Features
PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.
PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.
PepBuild
Protein >
3-D Structure Prediction
PepBuild is a tool that facilitates the construction, from known sequence and secondary/tertiary structures, of capped or uncapped proteins. The output generated is in PDB format.
PepBuild is a tool that facilitates the construction, from known sequence and secondary/tertiary structures, of capped or uncapped proteins. The output generated is in PDB format.
Phydbac2
Model Organisms >
Microbes
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.
PlasMapper
DNA >
Tools For the Bench
DNA > Utilities
Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats.
DNA > Utilities
Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats.
POBO
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
A server for the detection, comparison and verification of transcription factor binding site motifs in promoters. POBO bootstrap analysis applied to one or two clusters of co-regulated genes detects motifs under extreme levels of representation.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
A server for the detection, comparison and verification of transcription factor binding site motifs in promoters. POBO bootstrap analysis applied to one or two clusters of co-regulated genes detects motifs under extreme levels of representation.
PRED-GPCR
Protein >
Annotation and Function
Protein > Domains and Motifs
PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.
Protein > Domains and Motifs
PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.
PRED-TMBB
Protein >
2-D Structure Prediction
Protein > Localization and Targeting
PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.
Protein > Localization and Targeting
PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.
PredictProtein
Protein >
2-D Structure Prediction
Protein > Domains and Motifs
PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.
Protein > Domains and Motifs
PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.
PredictRegulon
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.
Expression > Gene Regulation
PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.
PrediSi
Protein >
Annotation and Function
Protein > Localization and Targeting
PrediSi (Prediction of Signal Peptides) takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome datasets.
Protein > Localization and Targeting
PrediSi (Prediction of Signal Peptides) takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome datasets.
ProbeLynx
DNA >
Tools For the Bench
Expression > Transcript Expression & Microarrays
Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.
Expression > Transcript Expression & Microarrays
Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.
PromoSer
DNA >
Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.
DNA > Structure and Sequence Feature Detection
Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.
ProMoST
Expression >
Protein Expression
Protein > Biochemical Features
Protein > Protein Expression
Protein > Proteomics
ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.
Protein > Biochemical Features
Protein > Protein Expression
Protein > Proteomics
ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.
ProSight PTM
Protein >
Biochemical Features
Protein > Proteomics
ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the 'Top-Down' tandem mass spectrometry (MS/MS) approach.
Protein > Proteomics
ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the 'Top-Down' tandem mass spectrometry (MS/MS) approach.
PROSPECT-PSPP
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses.
Protein > 3-D Structure Prediction
An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses.
ProteinDBS
Protein >
3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web.
Protein > 3-D Structure Retrieval, Viewing
ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web.
ProteMiner-SSM
Protein >
3-D Structure Comparison
ProteMiner-SSM searches the PDB for proteins with similar tertiary substructures to one specified by the user. A filtering process is used to significantly speed up the analysis.
ProteMiner-SSM searches the PDB for proteins with similar tertiary substructures to one specified by the user. A filtering process is used to significantly speed up the analysis.
Proteome Analyst
Protein >
Annotation and Function
Protein > Proteomics
Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers.
Protein > Proteomics
Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers.
PubCrawler
DNA >
Sequence Retrieval and Submission
Literature > Search Tools
Protein > Sequence Retrieval
RNA > Sequence Retrieval
It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).
Literature > Search Tools
Protein > Sequence Retrieval
RNA > Sequence Retrieval
It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).
PupaSuite
DNA >
Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.
Human Genome > Sequence Polymorphisms
PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.
pvSOAR
Protein >
3-D Structure Comparison
pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure.
pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure.
Qgrid
Protein >
Biochemical Features
Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins.
Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins.
RDfolder
RNA >
Structure Prediction, Visualization, and Design
A RNA secondary structure prediction program which implements two methods, one based on random stacking and the other based on helical region distributions.
A RNA secondary structure prediction program which implements two methods, one based on random stacking and the other based on helical region distributions.
RECON
DNA >
Structure and Sequence Feature Detection
RECON is a tool for calculating the probability of nucleosome formation along a DNA sequence input by the user.
RECON is a tool for calculating the probability of nucleosome formation along a DNA sequence input by the user.
Rescue-ESE
DNA >
Structure and Sequence Feature Detection
Expression > Splicing
Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.
Expression > Splicing
Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.
Riboswitch finder
Expression >
Gene Regulation
RNA > Motifs
RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.
RNA > Motifs
RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.
Robetta
Protein >
3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes
The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.
Protein > Interactions, Pathways, Enzymes
The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.
rVISTA
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.
Expression > Gene Regulation
Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.
SA-Search
Protein >
3-D Structure Comparison
SA-Search is a tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment.
SA-Search is a tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment.
SBT Interface - dbMHC
DNA >
Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes
The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes
The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.
SCit
Protein >
3-D Structural Features
SCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedral angles, listing structurally compatible rotamers for each residue and substituting side chains resulting in a new structure.
SCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedral angles, listing structurally compatible rotamers for each residue and substituting side chains resulting in a new structure.
SDPMOD
Protein >
3-D Structure Prediction
SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs).
SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs).
SDPpred
Protein >
Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences
SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences.
Sequence Comparison > Analysis of Aligned Sequences
SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences.
SeqVISTA
DNA >
Structure and Sequence Feature Detection
Sequence Comparison > Alignment Editing and Visualization
Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister.
Sequence Comparison > Alignment Editing and Visualization
Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister.
Sfold
DNA >
Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.
siDirect
DNA >
Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.
siRNA Selection Server
DNA >
Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA.
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA.
SITECON
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.
Expression > Gene Regulation
Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.
SledgeHMMER
Protein >
Domains and Motifs
SledgeHMMER is a tool for searching the Pfam database using a parallelized version of the program hmmpfam. The user can perform queries with one or more sequences at a time and then receive the results by e-mail.
SledgeHMMER is a tool for searching the Pfam database using a parallelized version of the program hmmpfam. The user can perform queries with one or more sequences at a time and then receive the results by e-mail.
SNPbox
DNA >
Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.
STRIDE
Protein >
2-D Structure Prediction
STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.
STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.
SuperPose
Protein >
3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules.
Protein > 3-D Structure Retrieval, Viewing
SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules.
T-COFFEE
DNA >
Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching
The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool that is more accurate than ClustalW for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. PROTOGENE turns amino acid alignments into CDS nucleotide alignments. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching
The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool that is more accurate than ClustalW for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. PROTOGENE turns amino acid alignments into CDS nucleotide alignments. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
The European Bioinformatics Institute (EBI)
DNA >
Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Transcript Expression & Microarrays
Protein > 3-D Structure Retrieval, Viewing
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures. The EBI web page is a portal to various public access databases and tools for information retrieval, analysis, and data submission provided by the EBI. The services include access to sequence, literature, microarray, and structure databases, and to tools such as BLAST, ClustalW, DALI, and InterProScan for sequence, structural and functional analysis. Various databases and software tools are also downloadable via FTP.
Education > Community
Education > Directories and Portals
Expression > Transcript Expression & Microarrays
Protein > 3-D Structure Retrieval, Viewing
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures. The EBI web page is a portal to various public access databases and tools for information retrieval, analysis, and data submission provided by the EBI. The services include access to sequence, literature, microarray, and structure databases, and to tools such as BLAST, ClustalW, DALI, and InterProScan for sequence, structural and functional analysis. Various databases and software tools are also downloadable via FTP.
TROD
DNA >
Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design
T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.
VISTA
DNA >
Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.
WAViS
DNA >
Utilities
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.
Web Weeder
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.
Expression > Gene Regulation
Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.
WebInterViewer
Protein >
Interactions, Pathways, Enzymes
WebInterViewer is a tool for visualizing molecular interaction networks. It employs a fast-layout algorithm, and can visualize data from interaction databases directly.
WebInterViewer is a tool for visualizing molecular interaction networks. It employs a fast-layout algorithm, and can visualize data from interaction databases directly.
Wurst
Protein >
3-D Structure Prediction
Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.
Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.
