Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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AAA: Amino Acid Analysis Server
[EMBL-Heidelberg] Protein and amino acid identification in SwissProt and PIR using amino acid composition.
[ExPASY] A tool used to identify a protein from its amino acid composition.
[ExPASY] Compares the amino acid composition of a SWISS-PROT entry with all other SWISS-PROT entries to find the proteins whose amino acid compositions are closest to that of the selected entry.
[Martin, UCL] Tests an antibody sequence against the Kabat sequence database.
AMAS: Analyze Multiple Alignments of Protein Sequences
[EBI] Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
[Institute of Biology and Chemistry of Proteins] (ANalyse THE PROTeins) This free software application integrates into a single package most of the methods designed for
protein sequence analysis. Methods include: Sequence information,
Sequence edition, dot matrix plot,
FASTA/BLAST, sites/signatures detection, physico-chemical profiles, secondary structure prediction, helical wheel projections, multiple alignments,
prediction of signal peptide and cleavage sites, 3D display of molecules, amphiphilicity, and
Atlas of Protein Side-Chain Interactions
[Univ. College London] Atlas depicts how amino acid side-chains pack against one another. Presents all possible 400 pairwise interactions between the 20 side chains.
BCM Search Launcher: Pairwise Sequence Alignment
[Baylor College of Medicine] A site with multiple tools to align pairs of input sequences.
Biomolecular Structure and Modelling Group
[University College London] The BSM group brings together people who derive protein and carbohydrate structure information using crystallography or NMR, those who manage databases of this information, and analysts and modellers who examine these structures to try to derive principles of protein folding. Services are offered in the areas of protein sequence and stucture analysis. The group is the home of the CATH protein structure classification database.
[CBS] Predicts whether or not an amino acid sequence contains an N-terminal chloroplast transit peptide, cTP, and the probable site for cleavage of the transit peptide.
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Clusters of Orthologous Groups
[NCBI] (COGs) A phylogenetic database (with a comparison search server incorporated) of orthologous proteins in many complete genomes.
[ExPASy] CombSearch is an attempt to provide a unified interface to query several protein identification tools accessible on the web. Includes PeptIdent, TagIdent, and MultiIdent from ExPASy, MS-Fit from ProteinProspector, Mowse from Imperial SERC Daresbury Laboratory, ProFound from PROWL, and Peptide Search from EMBL Protein & Peptide Group.
Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.
Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.
Compute pI/Mw tool
[ExPASY] A tool which allows the computation of the theoretical isoelectric point and molecular weight of a protein sequence.
CUBIC: Columbia University Bioinformatics Center
CUBIC contains a wealth of services, databases, articles and their data sets, and annotated bioinformatics links. It is the current home of PredictProtein and other services for protein analysis.
[Univ. of Tours] A program to generate peptide fragments by the enzymatic or chemical cleavage of a protein sequence entered by the user, and computes the theoretical masses to the generated peptides.
DARWIN Molecular Sequence Analysis
[CBRG] An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
[National Cancer Institute] This software is for information analysis of protein and nucleic-acid sequences.
[CBS] Produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
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[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences.
This downloadable package also has special functions for EST and SAGE handling and analysis.
[Karolinska Institutet, Center for Genomics Research] Compares two related sequences and finds matches, creating a dotplot. Accompanying the dotplot are excellent statistics and user-friendly adjustment of thresholds. Download the program to run on Unix. A server version is available at http://www.hgmp.mrc.ac.uk/Registered/Option/dotter.html for registered users.
Electron Density Server
[Uppsala University] Electron density calculations are based on the Protein Data Bank entries and deposited structure factors. The electron density maps derived from the structure factors and coordinates are
generated using the programs CNS or CCP4.
[Stanford Univ.] A protein identification tool allowing a protein sequence to be entered and submitted for identification.
[ExPASy] Predicts potential post-translational protein modifications (PTM) and finds potential single amino acid substitutions in peptides.
[European Bioinformatics Institute] "GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases."
[Washington Univ., St. Louis] A protein sequence analysis tool that profiles hidden Markov models (profile HMMs) that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
[Institute of Enzymology] Predicts transmembrane helices and topology of proteins.
Institute of Biology and Chemistry of Proteins
The aim of the research at the IBCP is to study proteins in their biological context. These studies are concerned with both intracellular and extracellular proteins of procaryotic and eucaryotic organisms dealing mainly with biosynthesis, maturation, and interactions. The IBCP is the home of Network Protein Sequence Analysis and software for protein sequence analysis.
[European Bioinformatics Institute] InterPro is an integrated documentation resource for protein families, domains and
sites, developed initially as a means of rationalising the complementary efforts of the
PROSITE, PRINTS, Pfam and ProDom database projects. Each combined InterPro
entry includes functional descriptions and literature references, and links are made
back to the relevant member database(s), allowing users to see at a glance whether
a particular family or domain has associated patterns, profiles, fingerprints, etc.
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ISREC Bioinformatics Group
[Swiss Institute for Experimental Cancer Research] "Our main field of research is the detection and assessment of similarity between distantly related protein and DNA sequences by means of 'Generalized Profiles.' We have developed and made available a program package that allows searches with a single sequence against a database of generalized profiles and vice versa."
ISREC Software Homepage
[Swiss Institute for Experimental Cancer] This site provides a number of servers in the areas of sequence analysis, domain/motif searches, gene prediction, and prediction of protein features.
[Univ. of York] MacStripe will explore potential alpha-helical coiled coils in the sequence of a protein.
[CBRG] A tool for searching SwissProt or EMBL by protein mass after digestion.
[Columbia University Bioinformatics Center] This server submits your protein sequence to other servers through one interface. Analyses are in the areas of protein structure and function.
[University of Minnesota] MetaFam is a comprehensive database of protein family information. This site contains functional assigments for
protein sequences and indicates the confidence of each assignment by
showing how all the other family databases have made the classification.
[ExPASy] Identifies proteins using pI, MW, amino acid composition, sequence tag, and peptide mass fingerprinting data.
NetOGlyc 2.0 Prediction Server
[Center for Biological Sequence Analysis] Produces neural network predictions of mucin type o-glycosylation sites in mammalian proteins.
[CBS] Produces neural network predictions of cleavage sites of picornaviral proteases.
Network Protein Sequence @nalysis
[Institute of Biology and Chemistry of Proteins] [email protected] is an interactive Web server dedicated to protein sequence analysis. Analyses offered include sequence similarity, site detection, multiple alignment, secondary structure prediction, and primary structure analysis. Analyses can be combined in a pipeline. The ANTHEPROT windows program is also available here.
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[Murdoch University] The Online Researchers Bioinformatics Interface Tools project was established to implement an easy to use web based
interface for registered members of the Murdoch Bioinformatics Research
Group (MBRG). The system provides interfaces to the server side programs BLAST, Repeat Masker, and ClustalW; while still providing a framework for many other programs to be added to the interface in
the future. This is a downloaded Java program.
PANAL Protein Analysis
[University of Minnesota] PANAL is an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the results as an intutive graphical summary.
[ExPASy] Cleaves one or more protein sequences from the SWISS-PROT and TrEMBL databases, or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the proteins.
[ExPASy] Identifies proteins using pI, MW, and peptide mass fingerprinting data.
[EMBL Protein & Peptide Group] A tool for protein database searching by mass spectrometric data, such as peptide mass maps or partial amino acid sequences.
PEST Sequence Utility
[Laboratory Research IT] Identifies PEST (proline, glutamic acid, serine, and threonine rich regions) regions in a submitted probe using Molecular faction of the P, E, S, and T components, and the hydrophobicity index of the region.
[Pathogenomics Project, Univ. British Columbia] Do molecular phylogenetics analysis of a protein sequence. Enter the sequence at the site. PhyloBLAST uses BLASTP to find related amino acid sequences in the Swiss-Prot database. Select those sequences desired, for a full phylogenetic analysis, satrting with a ClustalW multiple sequence alignment. A choice of Phylip programs, including parsimony, UPGMA, neighbor joining and distance matrix methods, produces a phylogenetic tree.
[consortium of several research laboratories] This genomics site is oriented to plant functional genomics. The site maintains servers for analyzing protein sequence, searching for patterns, and plotting motifs. The site also discusses plant protein phosphorylation.
[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.
[EMBL] PROPSEARCH was designed to find the putative protein family if querying a new sequence has failed using alignment methods. By neglecting the order of amino acid residues in a sequence, PROPSEARCH uses the amino acid composition instead.
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Protein Hydrophilicity/Hydrophobicity Search
[Weizmann Institute] Provides tools for plotting, comparing, and searching a library for similarities of a protein's hydropathy profile.
Protein Sequence Analysis Launcher
[Swedish Foundation for Strategic Research] At ProSAL you paste a single protein sequence and are offered analyses in the following areas: sequence similarity (local and global), domain and motif searches, and predictions of chemical and structural properties.
Protein Sequence Logos
[Technical Univ. of Denmark] (Jan Gorodkin) Performs protein sequence logos using relative entropy.
Protein Sequence Search Tool
[Indian Institute of Science] The service provides 6 utilities for analyzing protein sequences: sequence retrieval; amino acid composition, molecular wt., and volume; sequence length search; molecular weight search; identical pattern matching; and similar pattern matching.
[UCSF] Tools for mining sequence databases in conjunction with mass proteometry experiments.
[ExPASy] An extensive annotated list of links to tools that provide analysis of protein sequences and structures.
[ExPASy] A tool which allows the computation of various physical and chemical parameters for a given protein stored in SWISS-PROT or TrEMBL or for a user entered sequence. Parameters include molecular weight, theoretical pI, amino acid composition, extinction coefficient, estimated half-life, instability index, aliphatic index, and grand average of hydropathicity (GRAVY).
[ExPASy] Computes and represents the profile produced by any amino acid scale on a selected protein.
[Brunel University] "The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice, and receive the results of the prediction via E-mail. You may select one of three prediction methods to apply to your sequence: PSIPRED - a highly accurate secondary structure prediction method, MEMSAT 2 - a new version of our widely used transmembrane topology prediction method, and GenTHREADER - a new sequence profile based fold recognition method."
PSORT: Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences
[Osaka University] A WWW server for analyzing and predicting protein sorting signals coded in amino acid sequence.
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[The Hospital for Sick Children, Toronto] (Alex Dong Li) Searches for DNA or protein sequence repeats.
SAPS: Statistical Analysis of Protein Sequences
[ISREC] Analyzes proteins for statistically-significant features.
scan for matches
[Bioweb Pasteur] Search tool to search a protein or nucleic acid sequence for patterns. User may enter sequence or datafile to be searched, and sequence of pattern searched for.
Sequence Manipulation Site
The Sequence Manipulation Suite is a collection of web-based
programs for analyzing and formatting DNA and protein sequences. The output of each program is a set of HTML commands, which is
rendered by your web browser as a standard web page. You can print
and save the results, and you can edit them using an HTML editor or a
[CBS] Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.
SMART: Simple Modular Architecture Research Tool
[EMBL] Performs a search for proteins with specific combinations of domains in defined taxonomic ranges, and allows for rapid identification and annotation of signaling domain sequences.
SOPM Secondary Structure Prediction Method
[Pole Bio-Informatique Lyonnais] Makes a binary comparison of all protein sequences and takes into account the prediction of structural classes of proteins.
[Tokyo University] A tool for secondary structure prediction of membrane proteins from a protein sequence.
[The Barton Group] A suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position.
[ExPASy] Creates lists of proteins from one or more organisms that are within a user-specified pI or MW range. The program can also identify proteins from 2-D gels by virtue of their estimated pI, MW, and a short protein sequence tag of up to 6 amino acids.
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[Universität Tübingen] A LaTeX package for shading membrane protein topology plots.
[Karolinska Institutet] Tool for prediction of transmembrane segments in proteins.
[CBS] Predicts transmembrane helices in proteins.
[ISREC] Predicts transmembrane regions and orientation using a combination of several weight-matrices.