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ExPASy Proteomics tools

The tools marked by local are local to the ExPASy server. The remaining tools are developed and hosted on other servers.

[Protein identification and characterization] [DNA -> Protein] [Similarity searches] [Pattern and profile searches] [Post-translational modification prediction] [Topology prediction] [Primary structure analysis] [Secondary structure prediction] [Tertiary structure] [Sequence alignment] [Biological text analysis]

Protein identification and characterization
  • AACompIdent local - Identify a protein by its amino acid composition
  • AACompSim local - Compare the amino acid composition of a SWISS-PROT entry with all other entries
  • MultiIdent local - Identify proteins with pI, Mw, amino acid composition, sequence tag and peptide mass fingerprinting data
  • PeptIdent local - Identify proteins with peptide mass fingerprinting data, pI and Mw Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in SWISS-PROT, making extensive use of database annotations
  • TagIdent local - Identify proteins with pI, Mw and sequence tag, or generate a list of proteins close to a given pI and Mw
  • FindMod local - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified SWISS-PROT entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest.
  • GlycoMod local - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides)
  • GlycanMass local - Calculate the mass of an oligosaccharide structure
  • FindPept local - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage
  • PeptideMass local - Calculate masses of peptides and their post-translational modifications for a SWISS-PROT or TrEMBL entry or for a user sequence
  • PeptideCutter local - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence

  • PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK
  • Mascot - Peptide mass fingerprint, sequence query and MS/MS ion search from Matrix Science Ltd., London
  • PepSea - Protein identification by peptide mapping or peptide sequencing from Protana, Denmark
  • PeptideSearch - Peptide mass fingerprint tool from EMBL Heidelberg
  • ProteinProspector - A variety of tools from UCSF (MS-Fit, MS-Tag, MS-Digest, etc.) for mining sequence databases in conjunction with mass spectrometry experiments [Mirrors at UCL-Ludwig, UK / Ludwig Institute Melbourne (Australia)]
  • PROWL - Protein chemistry and mass spectrometry resource from Rockefeller and NY Universities

  • CombSearch local - An experimental unified interface to query several protein identification tools accessible on the web

DNA -> Protein
  • Translate local - Translates a nucleotide sequence to a protein sequence
  • Protein Machine - Nucleotide to protein translation at EBI
  • Transeq - Nucleotide to protein translation from the EMBOSS package
  • BCM search launcher - Six frame translation of nucleotide sequence(s)

  • Backtranslation - Translates a protein sequence back to a nucleotide sequence

  • Genewise - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
  • FSED - Frameshift error detection
  • LabOnWeb - Elongation, expression profiles and sequence analysis of ESTs using Compugen LEADS clusters

  • List of gene identification software sites

Similarity searches
  • BLAST and WU-BLAST - Interfaces to various versions of the Basic Local Alignment Search Tool
  • Bic ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator [At EBI, DKFZ or at Weizmann]
  • DeCypher - Smith/Waterman or FrameSearch search using the DeCypher hardware accelerator
  • Fasta3 - FASTA version 3 at the EBI
  • FDF - Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH
  • PropSearch; searches for structural homologs using a 'properties' approach [At EMBL or at Montpellier]
  • SAMBA - Systolic Accelerator for Molecular Biological Applications
  • SAWTED - Structure Assignment With Text Description
  • Scanps - Similarity searches using Barton's algorithm

Pattern and profile searches
  • InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases

  • ScanProsite local - Scans a sequence against PROSITE or a pattern against SWISS-PROT and TrEMBL
  • MotifScan - Scans a sequence against protein profile databases (including PROSITE)
  • Frame-ProfileScan - Scans a short DNA sequence against protein profile databases (including PROSITE)
  • Pfam HMM search; scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre]
  • FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database
  • FPAT - Regular expression searches in protein databases
  • PRATT - Interactively generates conserved patterns from a series of unaligned proteins
  • PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI
  • PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL
  • PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL
  • SMART - Simple Modular Architecture Research Tool; at EMBL
  • TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM

  • Hits - Relationships between protein sequences and motifs

Post-translational modification prediction
  • SignalP - Prediction of signal peptide cleavage sites
  • ChloroP - Prediction of chloroplast transit peptides
  • MITOPROT - Prediction of mitochondrial targeting sequences
  • Predotar - Prediction of mitochondrial and plastid targeting sequences

  • NetOGlyc - Prediction of type O-glycosylation sites in mammalian proteins
  • DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium
  • YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences

  • big-PI Predictor - GPI Modification Site Prediction
  • DGPI - Prediction of GPI-anchor and cleavage sites (Mirror site)
  • NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
  • NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins
  • NMT - Prediction of N-terminal N-myristoylation
  • Sulfinator local - Prediction of tyrosine sulfation sites

Topology prediction
  • PSORT - Prediction of protein sorting signals and localization sites
  • TargetP - Prediction of subcellular location

  • DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University)
  • HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences)
  • PredictProtein - Prediction of transmembrane helix location and topology (Columbia University)
  • SOSUI - Prediction of transmembrane regions (TUAT; Tokyo Univ. of Agriculture & Technology)
  • TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)
  • TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)
  • TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH)
  • TopPred 2 - Topology prediction of membrane proteins (Stockholm University)

Primary structure analysis
  • ProtParam local - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.)
  • Compute pI/Mw local - Compute the theoretical pI and Mw from a SWISS-PROT or TrEMBL entry or for a user sequence
  • MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve

  • REP - Searches a protein sequence for repeats
  • REPRO - De novo repeat detection in protein sequences
  • Radar - De novo repeat detection in protein sequences

  • SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]

  • Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL]
  • Paircoil - Prediction of coiled coil regions in proteins (Berger's method)
  • Multicoil - Prediction of two- and three-stranded coiled coils

  • PEST - Identification of PEST regions
  • PESTfind - Identification of PEST regions at EMBnet Austria

  • HLA_Bind - Prediction of MHC type I (HLA) peptide binding
  • SYFPEITHI - Prediction of MHC type I and II peptide binding

  • ProtScale local - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)
  • Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence
  • Protein Colourer - Tool for coloring your amino acid sequence
  • Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence
  • HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel

  • RandSeq local - Random protein sequence generator

Secondary structure prediction
  • AGADIR - An algorithm to predict the helical content of peptides
  • BCM PSSP - Baylor College of Medicine
  • Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction
  • GOR I (Garnier et al, 1978) [At PBIL or at SBDS]
  • GOR II (Gibrat et al, 1987)
  • GOR IV (Garnier et al, 1996)
  • HNN - Hierarchical Neural Network method (Guermeur, 1997)
  • Jpred - A consensus method for protein secondary structure prediction at EBI
  • nnPredict - University of California at San Francisco (UCSF)
  • PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University
  • PSA - BioMolecular Engineering Research Center (BMERC) / Boston
  • PSIpred - Various protein structure prediction methods at Brunel University
  • SOPM (Geourjon and Deléage, 1994)
  • SOPMA (Geourjon and Deléage, 1995)

Tertiary structure
  • SWISS-MODEL local - An automated knowledge-based protein modelling server
  • Geno3d - Automatic modelling of protein three-dimensional structure
  • CPHmodels - Automated neural-network based protein modelling server
  • 3D-PSSM - Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit)
  • ProSup - Protein structure superimposition
  • SWEET - Constructing 3D models of saccharids from their sequences
  • Swiss-PdbViewer local - A program to display, analyse and superimpose protein 3D structures

Sequence alignment
Binary
  • SIM + LALNVIEW local - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
  • LALIGN - Finds multiple matching subsegments in two sequences
  • Dotlet - A Java applet for sequence comparisons using the dot matrix method
Multiple
  • CLUSTALW [At EBI, PBIL or at EMBnet-CH]
  • T-Coffee [At EMBnet Switzerland or at CMBI]
  • ALIGN - at Genestream (IGH)
  • DIALIGN - Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany
  • Match-Box - at University of Namur, Belgium
  • MSA - at Washington University
  • Multalin [At INRA or at PBIL]
  • MUSCA - Multiple sequence alignment using pattern discovery, at IBM

  • AMAS - Analyse Multiply Aligned Sequences
  • Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building).
  • CINEMA - Color Interactive Editor for Multiple Alignments
  • ESPript - Tool to print a multiple alignment

  • plogo - Sequence logos at CBS/Denmark
  • GENIO/logo - Sequence logos at Stuttgart/Germany
  • WebLogo - Sequence logos at Cambridge/UK

    Biological text analysis
    • AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
    • AbXtract - A prototype system for the automatic annotation of functional characteristics in protein families
    • MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query
    • Protein Annotator's Assistant - A software system which assists protein annotators in the task of assigning functions to newly sequenced proteins
    • XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE

    Last modified 11/Sep/2002 by ELG

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