NAR Web Server Issue (July 1, 2007)
Source: http://nar.oxfordjournals.org/content/vol35/suppl_2/index.dtl
Total Links: 131
3D-partner
Protein >
3-D Structural Features
Protein > Interactions, Pathways, Enzymes
3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.
Protein > Interactions, Pathways, Enzymes
3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.
3dLOGO
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.
AStalavista
Expression >
Splicing
AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.
AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.
Asterias
DNA >
Annotations
Expression > Transcript Expression & Microarrays
Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.
Expression > Transcript Expression & Microarrays
Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.
Berkeley Phylogenomics Group
DNA >
Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.
BioBayesNet
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features
BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.
Expression > Gene Regulation
Protein > Sequence Features
BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.
BIPASS
Expression >
Splicing
BioInformatics Pipeline Alternative Splicing Services (BIPASS) provides access to alternative splicing information extracted from various public databases and allows users to submit their own transcript and genome sequences for alternative splicing predictions.
BioInformatics Pipeline Alternative Splicing Services (BIPASS) provides access to alternative splicing information extracted from various public databases and allows users to submit their own transcript and genome sequences for alternative splicing predictions.
BLASTO
DNA >
Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.
CanPredict
Human Genome >
Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features
CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.
Human Genome > Sequence Polymorphisms
Protein > Sequence Features
CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.
CARGO
DNA >
Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining
Protein > Interactions, Pathways, Enzymes
CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining
Protein > Interactions, Pathways, Enzymes
CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.
CodonO
DNA >
Structure and Sequence Feature Detection
Model Organisms > General Resources
CodonO is a method for measuring synonymous codon usage bias within and across genomes.
Model Organisms > General Resources
CodonO is a method for measuring synonymous codon usage bias within and across genomes.
COMPASS
Sequence Comparison >
Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching
COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.
Sequence Comparison > Similarity Searching
COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.
CPC
DNA >
Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs
CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs
CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.
CRISPRFinder
DNA >
Structure and Sequence Feature Detection
Model Organisms > Microbes
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.
Model Organisms > Microbes
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.
CrysTwiV
Protein >
3-D Structure Prediction
CrysTwiV (Crystal Twin Variables) is an automated approach for phase extension and refinement in X-ray crystallography; free registration is required for use.
CrysTwiV (Crystal Twin Variables) is an automated approach for phase extension and refinement in X-ray crystallography; free registration is required for use.
CytoSVM
Protein >
Interactions, Pathways, Enzymes
CytoSVM is a Support Vector Machine (SVM) based server that predicts putative cytokine-receptor interactions based on a primary protein sequence. Using this method, results from screening the human and mouse genomes are available via a database search.
CytoSVM is a Support Vector Machine (SVM) based server that predicts putative cytokine-receptor interactions based on a primary protein sequence. Using this method, results from screening the human and mouse genomes are available via a database search.
DAVID Bioinformatics Resources
DNA >
Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics
The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics
The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
DBAli
Protein >
3-D Structure Comparison
Protein > Annotation and Function
Protein > Domains and Motifs
DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.
Protein > Annotation and Function
Protein > Domains and Motifs
DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.
DEEP
Expression >
cDNA, EST, SAGE
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).
DIAL
RNA >
Motifs
RNA > Structure Prediction, Visualization, and Design
DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.
RNA > Structure Prediction, Visualization, and Design
DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.
DOMAC
Protein >
3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.
DSHIFT
DNA >
Structure and Sequence Feature Detection
DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.
DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.
EBI Tools
Computer Related >
Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.
eF-seek
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.
Protein > 3-D Structure Comparison
eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.
eProbalign
Sequence Comparison >
Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.
Sequence Comparison > Multiple Sequence Alignments
eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.
ESTExplorer
DNA >
Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.
ESTpass
DNA >
Annotations
DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching
ESTpass is a server for processing and annotating sequence data from expressed sequence tag (EST) projects.
DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching
ESTpass is a server for processing and annotating sequence data from expressed sequence tag (EST) projects.
eTBLAST
Literature >
Search Tools
eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.
eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.
EVALLER
Protein >
Annotation and Function
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
EVALLER predicts potential protein allergenicity from primary amino acid sequence.
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
EVALLER predicts potential protein allergenicity from primary amino acid sequence.
FastContact
Protein >
Molecular Dynamics and Docking
FastContact is a free energy scoring tool for protein-protein complex structures.
FastContact is a free energy scoring tool for protein-protein complex structures.
fastSCOP
Protein >
3-D Structure Comparison
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.
FatiGOplus
DNA >
Annotations
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.
FGF
Protein >
Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).
firestar
Protein >
3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
Firestar predicts functionally important residues, such as ligand binding sites, using structural templates and alignment reliability.
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
Firestar predicts functionally important residues, such as ligand binding sites, using structural templates and alignment reliability.
FluGenome
Human Genome >
Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching
FluGenome is a tool for determining lineages and genotypes of influenza A viruses.
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching
FluGenome is a tool for determining lineages and genotypes of influenza A viruses.
FRalanyzer
Protein >
2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Sequence Comparison > Analysis of Aligned Sequences
FRalanyzer (Fold Recognition alignment analyzer) takes as input a sequence-structure alignment, automatically searches annotated databases, and highlights the functionally important positions that are identical in the alignment.
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Sequence Comparison > Analysis of Aligned Sequences
FRalanyzer (Fold Recognition alignment analyzer) takes as input a sequence-structure alignment, automatically searches annotated databases, and highlights the functionally important positions that are identical in the alignment.
Frog
Other Molecules >
Small Molecules
Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).
Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).
G2D
Human Genome >
Health and Disease
G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.
G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.
g:Profiler
DNA >
Annotations
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles.
GeneHub-GEPIS
Expression >
cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat
GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.
Human Genome > Other Resources
Model Organisms > Mouse and Rat
GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.
GeneTrail
DNA >
Annotations
Expression > Transcript Expression & Microarrays
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting
GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.
Expression > Transcript Expression & Microarrays
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting
GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.
Gibbs Motif Sampler
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).
Expression > Gene Regulation
Protein > Domains and Motifs
Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).
iHOP
Literature >
Text Mining
Protein > Interactions, Pathways, Enzymes
iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.
Protein > Interactions, Pathways, Enzymes
iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.
INDELSCAN
DNA >
Annotations
Sequence Comparison > Analysis of Aligned Sequences
INDELSCAN is a tool for genome-wide identification of indels.
Sequence Comparison > Analysis of Aligned Sequences
INDELSCAN is a tool for genome-wide identification of indels.
INFO-RNA
RNA >
Structure Prediction, Visualization, and Design
INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
iPDA
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.
Protein > 3-D Structure Prediction
iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.
ISACGH
Expression >
Transcript Expression & Microarrays
ISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package.
ISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package.
KAAS
DNA >
Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics
KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics
KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.
KinasePhos 2.0
Protein >
Domains and Motifs
KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.
KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.
KNOTS
Protein >
3-D Structural Features
KNOTS is a web server that detects knots in protein structures.
KNOTS is a web server that detects knots in protein structures.
LIPID MAPS
Human Genome >
Other Resources
Other Molecules > Metabolites
LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.
Other Molecules > Metabolites
LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.
LTR_Finder
DNA >
Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Plants
LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.
DNA > Structure and Sequence Feature Detection
Model Organisms > Plants
LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.
M4T
Protein >
3-D Structure Prediction
M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.
M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.
MADAP
DNA >
Annotations
Expression > Gene Regulation
Human Genome > Annotations
MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5' and 3'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).
Expression > Gene Regulation
Human Genome > Annotations
MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5' and 3'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).
MAGMA
Expression >
Transcript Expression & Microarrays
MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.
MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.
MelinaII
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.
Expression > Gene Regulation
Protein > Domains and Motifs
MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.
MetaPath Online
Other Molecules >
Metabolites
Protein > Interactions, Pathways, Enzymes
MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.
Protein > Interactions, Pathways, Enzymes
MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.
MinActionPath
Protein >
3-D Structure Retrieval, Viewing
Protein > Molecular Dynamics and Docking
MinActionPath calculates the most-probable trajectory between two known structural states of a protein.
Protein > Molecular Dynamics and Docking
MinActionPath calculates the most-probable trajectory between two known structural states of a protein.
miPred
RNA >
Functional RNAs
miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.
miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.
MobilomeFINDER
Model Organisms >
Microbes
MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.
MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.
MODPROPEP
Protein >
3-D Structure Prediction
Protein > Domains and Motifs
MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.
Protein > Domains and Motifs
MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.
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.
Multi-Q
Protein >
Proteomics
Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.
Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.
MultiPhyl
DNA >
Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.
MYBS
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Yeast
MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.
Expression > Gene Regulation
Model Organisms > Yeast
MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.
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.
NCBI Influenza Virus Sequence Annotation Tool
DNA >
Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms
The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms
The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.
NQ-Flipper
Protein >
3-D Structure Prediction
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.
NTMG
DNA >
Tools For the Bench
NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.
NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.
OligoCalc
DNA >
Tools For the Bench
OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation.
OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation.
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.
OpenHUSAR
Protein >
2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching
Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching
Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).
oPOSSUM
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.
Expression > Gene Regulation
oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.
OPTIMIZER
DNA >
Structure and Sequence Feature Detection
Expression > Protein Expression
OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.
Expression > Protein Expression
OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.
OSCAR
Expression >
Transcript Expression & Microarrays
OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.
OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.
PAP
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.
PAR-3D
Protein >
3-D Structural Features
Protein > Annotation and Function
PAR-3D (Protein Active site Residues - 3D structural motif) uses a structure-based approach for predicting function. Using 3D structural motifs defined for different classes of proteases, glycolytic pathway enzymes and metal-binding sites, PAR-3D predicts probable active site residues.
Protein > Annotation and Function
PAR-3D (Protein Active site Residues - 3D structural motif) uses a structure-based approach for predicting function. Using 3D structural motifs defined for different classes of proteases, glycolytic pathway enzymes and metal-binding sites, PAR-3D predicts probable active site residues.
PathExpress
Expression >
Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.
Protein > Interactions, Pathways, Enzymes
PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.
Pcons.net
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.
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.
PFP
Protein >
3-D Structural Features
Protein > Interactions, Pathways, Enzymes
PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.
Protein > Interactions, Pathways, Enzymes
PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.
Phobius
Protein >
2-D Structure Prediction
Protein > Localization and Targeting
Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.
Protein > Localization and Targeting
Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.
Phylemon
DNA >
Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs.
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs.
PI2PE
Protein >
3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.
PIC
Protein >
3-D Structural Features
Protein > Interactions, Pathways, Enzymes
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.
Protein > Interactions, Pathways, Enzymes
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.
pKNOT
Protein >
3-D Structural Features
pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB.
pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB.
pknotsRG
RNA >
Structure Prediction, Visualization, and Design
pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.
pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.
PMG
Protein >
3-D Structure Retrieval, Viewing
The Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies.
The Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies.
PrDOS
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.
Protein > 3-D Structure Prediction
PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.
Primer Z
DNA >
Tools For the Bench
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat
Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat
Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.
Primer3Plus
DNA >
Tools For the Bench
Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.
Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.
PROMALS and PROMALS3D
Sequence Comparison >
Multiple Sequence Alignments
PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.
PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.
ProMateus
Protein >
3-D Structural Features
Protein > Interactions, Pathways, Enzymes
ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.
Protein > Interactions, Pathways, Enzymes
ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.
ProSA-web
Protein >
3-D Structure Prediction
ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.
ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.
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.
Protein Dipole Server
Protein >
3-D Structural Features
Protein > Biochemical Features
The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.
Protein > Biochemical Features
The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.
QSCOP - BLAST
Protein >
3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching
QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).
QuickSNP
DNA >
Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.
Human Genome > Sequence Polymorphisms
QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.
RADAR
RNA >
Motifs
RNA > Structure Prediction, Visualization, and Design
RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.
RNA > Structure Prediction, Visualization, and Design
RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.
RCI
Protein >
3-D Structural Features
Protein > 3-D Structure Prediction
RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.
Protein > 3-D Structure Prediction
RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.
RE-MuSiC
Protein >
Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
RE-MuSiC is a tool for multiple sequence alignments where users can specify conserved blocks by supplying regular expression contraints.
Sequence Comparison > Multiple Sequence Alignments
RE-MuSiC is a tool for multiple sequence alignments where users can specify conserved blocks by supplying regular expression contraints.
REPK
DNA >
Tools For the Bench
Model Organisms > Microbes
REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.
Model Organisms > Microbes
REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.
RF_DYMHC
DNA >
Structure and Sequence Feature Detection
Model Organisms > Yeast
RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.
Model Organisms > Yeast
RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.
RNA Movies
RNA >
Structure Prediction, Visualization, and Design
RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.
RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.
RNABindR
Protein >
Domains and Motifs
RNABindR is a server for analyzing and predicting RNA binding sites in proteins.
RNABindR is a server for analyzing and predicting RNA binding sites in proteins.
RNAbor
RNA >
Structure Prediction, Visualization, and Design
RNAbor is a server for computing structural neighbors of a RNA secondary structure.
RNAbor is a server for computing structural neighbors of a RNA secondary structure.
RNAz
RNA >
Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences
RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.
Sequence Comparison > Analysis of Aligned Sequences
RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.
RSRE
RNA >
Structure Prediction, Visualization, and Design
RNA Structural Robustness Evaluator (RSRE) is a tool for RNA structural robustness evaluation.
RNA Structural Robustness Evaluator (RSRE) is a tool for RNA structural robustness evaluation.
RTAnalyzer
DNA >
Annotations
DNA > Structure and Sequence Feature Detection
RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.
DNA > Structure and Sequence Feature Detection
RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.
SAGExplore
DNA >
Annotations
Expression > cDNA, EST, SAGE
Model Organisms > Yeast
SAGExplore is a tool for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE).
Expression > cDNA, EST, SAGE
Model Organisms > Yeast
SAGExplore is a tool for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE).
SCOPE
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences.
Expression > Gene Regulation
SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences.
Selecton
DNA >
Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Selecton is a server for the identification of site-specific positive selection and purifying selection.
Sequence Comparison > Analysis of Aligned Sequences
Selecton is a server for the identification of site-specific positive selection and purifying selection.
SEPACS
Protein >
Annotation and Function
SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.
SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.
Sequence Harmony
Protein >
Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences
Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.
Sequence Comparison > Analysis of Aligned Sequences
Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.
SH3-Hunter
Protein >
Domains and Motifs
Protein > Interactions, Pathways, Enzymes
SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.
Protein > Interactions, Pathways, Enzymes
SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.
SiteFINDER|3D
Protein >
3-D Structural Features
Sequence Comparison > Analysis of Aligned Sequences
SiteFINDER|3D predicts functionally important regions in proteins of known structure using conserved functional group (CFG) analysis.
Sequence Comparison > Analysis of Aligned Sequences
SiteFINDER|3D predicts functionally important regions in proteins of known structure using conserved functional group (CFG) analysis.
SLiMDisc
Protein >
Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting
SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting
SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.
SplicePort
Expression >
Splicing
SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.
SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.
STAMP
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.
Expression > Gene Regulation
STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.
StSNP
DNA >
Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes
StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.
Human Genome > Sequence Polymorphisms
Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes
StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.
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.
taveRNA
RNA >
Functional RNAs
RNA > Structure Prediction, Visualization, and Design
taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.
RNA > Structure Prediction, Visualization, and Design
taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.
TFAM
RNA >
Functional RNAs
TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.
TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.
VisANT
Expression >
Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.
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.
WebMOTIFS
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.
WebTraceMiner
DNA >
Tools For the Bench
Expression > cDNA, EST, SAGE
WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3' and 5' termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.
Expression > cDNA, EST, SAGE
WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3' and 5' termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.
WhETS
DNA >
Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching
WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching
WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.
WoLF PSORT
Protein >
Localization and Targeting
WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.
WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.
ZiFiT
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences; free registration is required.
Expression > Gene Regulation
ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences; free registration is required.
