NAR Web Server Issue (July 1, 2003)
Source: http://nar.oxfordjournals.org/content/vol31/issue13/
Total Links: 129
3D-Jury
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.
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.
3Matrix
Protein >
3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.
Protein > Domains and Motifs
3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.
3Motif
Protein >
3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.
Protein > Domains and Motifs
3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.
AHMII
Model Organisms >
Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast
Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.
Model Organisms > Other Organisms
Model Organisms > Yeast
Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.
ALGGEN
DNA >
Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Expression > Gene Regulation
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.
Expression > cDNA, EST, SAGE
Expression > Gene Regulation
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.
AMIGene
DNA >
Gene Prediction
Model Organisms > Microbes
Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.
Model Organisms > Microbes
Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.
Andrej Sali Lab
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking
This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking
This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).
Bioverse
DNA >
Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval
Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval
Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.
BLAST2SRS
Protein >
Sequence Retrieval
Sequence Comparison > Similarity Searching
BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.
Sequence Comparison > Similarity Searching
BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.
BPROMPT
Protein >
2-D Structure Prediction
Protein > Localization and Targeting
Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.
Protein > Localization and Targeting
Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.
CASTp
Protein >
3-D Structural Features
Protein > 3-D Structure Retrieval, Viewing
Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.
Protein > 3-D Structure Retrieval, Viewing
Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.
ChipInfo
Expression >
Transcript Expression & Microarrays
ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.
ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.
CLOURE
Sequence Comparison >
Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
CLustal OUtput REformatter (CLOURE) is a tool for highlighting sequence differences in CLUSTAL alignments.
Sequence Comparison > Analysis of Aligned Sequences
CLustal OUtput REformatter (CLOURE) is a tool for highlighting sequence differences in CLUSTAL alignments.
Cluster Buster
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.
Expression > Gene Regulation
Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.
CODEHOP
DNA >
Tools For the Bench
COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.
COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.
CRP
Protein >
Domains and Motifs
Protein > Sequence Features
Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.
Protein > Sequence Features
Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.
DePIE
DNA >
Tools For the Bench
Protein > Interactions, Pathways, Enzymes
Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.
Protein > Interactions, Pathways, Enzymes
Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.
DEREF
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Dragon Estrogen Response Element Finder (DEREF) allows the discovery of transcription factor binding sites (TFBS) in vertebrate genomic sequences.
Expression > Gene Regulation
Dragon Estrogen Response Element Finder (DEREF) allows the discovery of transcription factor binding sites (TFBS) in vertebrate genomic sequences.
DGSF
DNA >
Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Dragon Gene Start Finder (DGSF) predicts promoters and transcription start sites (TSS) within CpG islands for mammalian DNA sequences.
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Dragon Gene Start Finder (DGSF) predicts promoters and transcription start sites (TSS) within CpG islands for mammalian DNA sequences.
DNannotator
DNA >
Annotations
Human Genome > Annotations
DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).
Human Genome > Annotations
DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).
DNAtools
DNA >
Gene Prediction
DNA > Utilities
DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.
DNA > Utilities
DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.
DSSPcont
Protein >
2-D Structure Prediction
DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.
DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.
ELM
Protein >
Domains and Motifs
Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.
Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.
ENDscript
Protein >
2-D Structure Prediction
Protein > 3-D Structure Retrieval, Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.
Protein > 3-D Structure Retrieval, Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.
EnteriX
Model Organisms >
Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.
ESEfinder
Expression >
Splicing
ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.
ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.
ESPript
Sequence Comparison >
Alignment Editing and Visualization
Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.
Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.
EUGENE'HOM
DNA >
Annotations
DNA > Gene Prediction
Model Organisms > Plants
EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.
DNA > Gene Prediction
Model Organisms > Plants
EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.
EVA
Computer Related >
Statistics
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.
ExPASy Molecular Biology Server
Education >
Directories and Portals
Protein > Do-it-all Tools for Protein
Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.
Protein > Do-it-all Tools for Protein
Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.
ExpressYourself
Expression >
Transcript Expression & Microarrays
ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.
ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.
FIE2.0
DNA >
Sequence Retrieval and Submission
Expression > Gene Regulation
5' end Information Extraction v2 (FIE2) identifies and extracts nucleotide sequence around the promoter region of genes and their translation initiation sites (TIS). User can search by gene/protein name or Locus ID.
Expression > Gene Regulation
5' end Information Extraction v2 (FIE2) identifies and extracts nucleotide sequence around the promoter region of genes and their translation initiation sites (TIS). User can search by gene/protein name or Locus ID.
FootPrinter
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Comparative Genomics
FootPrinter is a program for phylogenetic footprinting that identifies regions of DNA that are well conserved across a set of orthologous sequences in order to infer phylogenetic relationships.
Expression > Gene Regulation
Sequence Comparison > Comparative Genomics
FootPrinter is a program for phylogenetic footprinting that identifies regions of DNA that are well conserved across a set of orthologous sequences in order to infer phylogenetic relationships.
FrameD
DNA >
Gene Prediction
FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.
FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.
GeneFizz
DNA >
Gene Prediction
GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.
GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.
GenePublisher
Expression >
Transcript Expression & Microarrays
GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.
GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.
GeneSeqer
DNA >
Gene Prediction
Expression > Splicing
Model Organisms > Plants
GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.
Expression > Splicing
Model Organisms > Plants
GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.
GeneSilico
Protein >
3-D Structure Prediction
GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers.
GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers.
Geno2pheno
Model Organisms >
Other Organisms
Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.
Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.
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.
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. 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. Can be applied for the detection of transcription factor binding sites (TFBS).
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).
GlobPlot
Protein >
2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Domains and Motifs
GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.
Protein > 3-D Structural Features
Protein > Domains and Motifs
GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.
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.
GPRM
RNA >
Structure Prediction, Visualization, and Design
Genetic Programming for RNA Motifs (GPRM) finds common secondary structure elements in a set of unaligned RNA sequences.
Genetic Programming for RNA Motifs (GPRM) finds common secondary structure elements in a set of unaligned RNA sequences.
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.
INCLUSive
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
Institute of Enzymology Servers
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.
iSPOT
Protein >
Domains and Motifs
Protein > Interactions, Pathways, Enzymes
iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.
Protein > Interactions, Pathways, Enzymes
iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.
JVirGel
Expression >
Protein Expression
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics
JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics
JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.
LGA
Protein >
3-D Structure Comparison
Local-Global Alignment (LGA) performs structural alignments for two proteins structures or fragments of 3D protein structures.
Local-Global Alignment (LGA) performs structural alignments for two proteins structures or fragments of 3D protein structures.
LNAtools
DNA >
Sequence Polymorphisms
DNA > Tools For the Bench
Expression > Transcript Expression & Microarrays
RNA > Structure Prediction, Visualization, and Design
LNAtools is a collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis; secondary structure prediction; and probe design for expression arrays, real time PCR, and SNP genotyping.
DNA > Tools For the Bench
Expression > Transcript Expression & Microarrays
RNA > Structure Prediction, Visualization, and Design
LNAtools is a collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis; secondary structure prediction; and probe design for expression arrays, real time PCR, and SNP genotyping.
Loc3D
Protein >
Localization and Targeting
LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.
LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.
MAK
DNA >
Structure and Sequence Feature Detection
MAK is a tool for detecting miniature inverted repeat transposable elements (MITEs). Given the sequence of a MITE element, MAK can retrieve and orient sequences of other members of the family, identify genes closest to the MITE elements, and can predict the anchor element for the MITE family.
MAK is a tool for detecting miniature inverted repeat transposable elements (MITEs). Given the sequence of a MITE element, MAK can retrieve and orient sequences of other members of the family, identify genes closest to the MITE elements, and can predict the anchor element for the MITE family.
Match
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.
Expression > Gene Regulation
Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.
MATRAS
Protein >
3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.
MAVID
DNA >
Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.
Meta-PP
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
Single interface providing access to a select subset of prediction servers (Motifs, 1D, 3D). It allows a single sequence entry to generate results from selected servers simultaneously.
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
Single interface providing access to a select subset of prediction servers (Motifs, 1D, 3D). It allows a single sequence entry to generate results from selected servers simultaneously.
Mfold
RNA >
Structure Prediction, Visualization, and Design
Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.
Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.
MGAlignIt
Sequence Comparison >
Other Alignment Tools
mRNA to Genome Alignments (MgAlignIt) aligns mRNA/EST to genome sequences and visualizes the alignment to provides intron/exon structure information.
mRNA to Genome Alignments (MgAlignIt) aligns mRNA/EST to genome sequences and visualizes the alignment to provides intron/exon structure information.
MHCPred
DNA >
Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes
Major Histocompatibility Complex Predictor (MHCPred) predicts the binding affinities of major histocompatibility complexes to ligands.
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes
Major Histocompatibility Complex Predictor (MHCPred) predicts the binding affinities of major histocompatibility complexes to ligands.
Modeller
Protein >
3-D Structure Prediction
Homology or comparative modeling of 3D protein structures.
Homology or comparative modeling of 3D protein structures.
MolSurfer
Protein >
3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.
Motif3D
Protein >
3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.
Protein > Domains and Motifs
Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.
mreps
DNA >
Structure and Sequence Feature Detection
mreps is a tool for identifing tandemn repeats in DNA sequences.
mreps is a tool for identifing tandemn repeats in DNA sequences.
NDB Tools
RNA >
Motifs
RNA > Structure Prediction, Visualization, and Design
The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.
RNA > Structure Prediction, Visualization, and Design
The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.
NEBcutter
DNA >
Tools For the Bench
NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.
NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.
NEWT
DNA >
Phylogeny Reconstruction
Model Organisms > General Resources
Protein > Phylogeny Reconstruction
NEWT is the taxonomy database maintained by the UniProt group.
Model Organisms > General Resources
Protein > Phylogeny Reconstruction
NEWT is the taxonomy database maintained by the UniProt group.
NORSp
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.
Protein > 3-D Structure Prediction
NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.
NRSAS
Protein >
3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval, Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features
Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval, Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features
Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.
OligoWiz
DNA >
Tools For the Bench
Expression > Transcript Expression & Microarrays
OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.
Expression > Transcript Expression & Microarrays
OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.
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.
PARSESNP
DNA >
Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.
PatSearch
DNA >
Structure and Sequence Feature Detection
Protein > Domains and Motifs
RNA > Motifs
PatSearch is a pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices.
Protein > Domains and Motifs
RNA > Motifs
PatSearch is a pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices.
PBIL
Education >
Directories and Portals
Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.
Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.
PDA
DNA >
Tools For the Bench
Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.
Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.
Pfold
RNA >
Structure Prediction, Visualization, and Design
The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.
The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.
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.
PINTS
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.
PipeAlign
Protein >
Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.
PipMaker
Sequence Comparison >
Analysis of Aligned Sequences
PipMaker computes alignments of similar regions in two DNA sequences. MultiPipMaker allows the user to see relationships among more than two sequences.
PipMaker computes alignments of similar regions in two DNA sequences. MultiPipMaker allows the user to see relationships among more than two sequences.
POPS
Protein >
3-D Structural Features
Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.
Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.
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.
PromH
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.
Expression > Gene Regulation
PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.
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.
Protinfo
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.
Protein > 3-D Structure Prediction
Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.
PSEUDOVIEWER
RNA >
Structure Prediction, Visualization, and Design
PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.
PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.
PSORT.org
Protein >
Localization and Targeting
PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.
PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.
RbDe
Protein >
2-D Structure Prediction
Protein > Presentation and Format
Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.
Protein > Presentation and Format
Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.
REDUCE
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.
Expression > Gene Regulation
Expression > Transcript Expression & Microarrays
REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.
RevTrans
Sequence Comparison >
Multiple Sequence Alignments
RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.
RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.
rMotif
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Yeast
rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).
Expression > Gene Regulation
Model Organisms > Yeast
rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).
RNA Analyzer
RNA >
Motifs
RNA > Structure Prediction, Visualization, and Design
RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.
RNA > Structure Prediction, Visualization, and Design
RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.
RNA Studio
RNA >
General Resources
RNA > Structure Prediction, Visualization, and Design
RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization.
RNA > Structure Prediction, Visualization, and Design
RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization.
RNAsoft
RNA >
Structure Prediction, Visualization, and Design
Software for RNA/DNA secondary structure prediction and design
Software for RNA/DNA secondary structure prediction and design
RSAT
DNA >
Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
DNA > Utilities
Expression > Gene Regulation
Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows.
DNA > Structure and Sequence Feature Detection
DNA > Utilities
Expression > Gene Regulation
Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows.
Scansite
Protein >
Domains and Motifs
Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.
Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.
SEARCHPKS
Protein >
Domains and Motifs
SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.
SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.
SEM
Protein >
3-D Structure Retrieval, Viewing
RNA > Structure Prediction, Visualization, and Design
Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary.
RNA > Structure Prediction, Visualization, and Design
Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary.
SIFT
DNA >
Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function
Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function
Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.
SIRW
Protein >
Domains and Motifs
Protein > Sequence Retrieval
SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif.
Protein > Sequence Retrieval
SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif.
SiteSeer
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.
Expression > Gene Regulation
SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.
SLAM
DNA >
Gene Prediction
DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
SLAM is a comparative-based annotation and alignment tool for syntenic genomic sequences that performs gene finding and alignment simultaneously. SLAM also predicts CNSs (conserved non-coding sequences).
DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
SLAM is a comparative-based annotation and alignment tool for syntenic genomic sequences that performs gene finding and alignment simultaneously. SLAM also predicts CNSs (conserved non-coding sequences).
SMS
Protein >
3-D Structure Prediction
STING Millennium Suite (SMS) is a web-based collection of programs and databases providing visualization and structural analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). Some analysis features include quality of the structure, nature and volume of atomic contacts of intra and inter chain type, and relative conservation of amino acids at the specific sequence position based on multiple sequence alignment.
STING Millennium Suite (SMS) is a web-based collection of programs and databases providing visualization and structural analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). Some analysis features include quality of the structure, nature and volume of atomic contacts of intra and inter chain type, and relative conservation of amino acids at the specific sequence position based on multiple sequence alignment.
SPatt
DNA >
Structure and Sequence Feature Detection
Statistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences.
Statistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences.
SSA
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).
Expression > Gene Regulation
Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).
SSEP
Protein >
2-D Structure Prediction
Secondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.
Secondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.
STING Millenium
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.
SVM-PROT
Protein >
Domains and Motifs
Protein > Sequence Features
Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.
Protein > Sequence Features
Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.
Swiss EMBnet
Education >
Directories and Portals
Swiss EMBnet is a web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics.
Swiss EMBnet is a web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics.
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.
Target Explorer
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Fly
Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.
Expression > Gene Regulation
Model Organisms > Fly
Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.
The Mendel Site
Protein >
Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.
Protein > Domains and Motifs
Protein > Localization and Targeting
The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.
TIGR Software Tools
DNA >
Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression & Microarrays
Sequence Comparison > Comparative Genomics
A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression & Microarrays
Sequence Comparison > Comparative Genomics
A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).
TMH Benchmark
Protein >
2-D Structure Prediction
Protein > Localization and Targeting
The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.
Protein > Localization and Targeting
The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.
TRACTS
DNA >
Gene Prediction
DNA > Structure and Sequence Feature Detection
TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.
DNA > Structure and Sequence Feature Detection
TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.
UniqueProt
Protein >
Sequence Retrieval
UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine.
UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine.
VADAR
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.
Protein > 3-D Structure Prediction
Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.
Vienna RNA Package
RNA >
Structure Prediction, Visualization, and Design
Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
WEB-THERMODYN
DNA >
Structure and Sequence Feature Detection
WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.
WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.
WebFEATURE
Protein >
3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design
WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design
WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.
WebSIC
DNA >
Structure and Sequence Feature Detection
Scan Inverse Complementary (SIC) provides a tool for detecting short inverted segments in a DNA sequence.
Scan Inverse Complementary (SIC) provides a tool for detecting short inverted segments in a DNA sequence.
WU BLAST
DNA >
Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching
Washington University Basic Local Alignment Search Tool
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching
Washington University Basic Local Alignment Search Tool
XML Central of DDBJ
Computer Related >
Web Services
Education > Directories and Portals
XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.
Education > Directories and Portals
XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.
XplorMed
Literature >
Search Tools
Literature > Text Mining
XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion.
Literature > Text Mining
XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion.
YMF 3.0
DNA >
Structure and Sequence Feature Detection
YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.
YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.
