ExPASy tools menu

Sequence analysis tools

• Protein Identification
  • Swiss-Shop - a sequence alerting system for SWISS-PROT that allows you to automatically obtain (by email) new sequence entries relevant to your field(s) of interest
  • AACompIdent - Identify a protein by its amino acid composition
  • AACompSim - Compare the amino acid composition of a SWISS-PROT entry with all other entries
  • MultiIdent - Identify proteins with pI, MW, amino acid compositon, sequence tag and peptide mass fingerprinting data
  • TagIdent (previously GuessProt) - Get the SWISS-PROT proteins closest to a given pI and Mw and identify proteins with a sequence tag
  • PeptideMass - Calculate masses of peptides and their posttranslational modifications for a SWISS-PROT entry or for a user sequence
  • Compute pI/Mw - Compute the theoretical pI and Mw from a SWISS-PROT entry or for a user sequence

  • ProteinProspector - A variety of tools from UCSF (MS-Fit, MS-Tag, MS-Digest, etc.) for mining sequence databases in conjunction with Mass Proteometry experiments [See also the mirror in UCL-Ludwig in the UK]
  • PROWL - Protein information Retrieval On-line WWW Lab from the MS groups at Rockefeller and NY Universities
  • PeptideSearch - Peptide mass fingerprint tool from EMBL Heidelberg

• DNA -> Protein
  • Translate - Translate a nucleotide sequence to a protein
  • Protein machine - Nucleotide to protein translation at EBI

• Similarity searches
  • BLAST and WU-BLAST - Interfaces to various versions of the Basic Local Alignment Search Tool
    • Local interface to BLAST at NCBI
    • Original interface of BLAST at NCBI
    • Local interface to WU-BLAST at EMBNet-CH (Lausanne)
    • Original interface to WU-BLAST at EMBNet-CH (Lausanne)
    • WU-BLAST at Bork's group in EMBL (Heidelberg)
    • WU-BLAST and BLAST at the EBI (Hinxton)
  • BLITZ - EBI's ultra-fast protein database searches using MPsearch
  • Bic - Ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator at Weizmann or at the EBI
  • BioSCAN - Biological Sequence Comparative Analysis at U. North Carolina
  • DeCypher II - Smith-Waterman search using the DeCypher hardware accelerator
  • Fasta3 - FASTA version 3 at the EBI
  • PropSearch - Search for structural homologs using a 'properties' approach

• Pattern and profile searches
  • ScanProsite - Scan a sequence against PROSITE or a pattern against SWISS-PROT
  • ProfileScan - Scan a sequence against the profile entries in PROSITE
  • Pfam-A HMM search - Scan a sequence against the PFAM HMM protein families db
  • FPAT - Regular expression searches in protein databases
  • PRATT - Interactively generates conserved patterns from a series of unaligned proteins

• Primary structure analysis
  • ProtParam - Physico-chemical parameters of a protein sequence (composition, extinction coefficient, etc.)
  • ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)
  • SAPS - Statistical analysis of protein sequences at ISREC [Also available at EBI]
  • PSORT - Prediction of protein sorting signals and localization sites
  • Signalp - Prediction of the signal peptide cleavage sites
  • NetOglyc - Prediction of type O-glycosylation sites in mammalian proteins
  • Coils - Prediction of coiled coil regions in proteins (Lupas's method)
  • Paircoil - Prediction of coiled coil regions in proteins (Berger's method)
  • REPRO - Recognition of protein sequence repeats at EMBL
  • Protein Colourer - Tool for colouring your amino acid sequence
  • RandSeq - Random protein sequence generator

• Secondary structure prediction
  • AntheProt - Institute of Biology and Chemistry of Proteins (IBCP) / Lyon
  • BCM PSSP - Baylor College of Medicine
  • DSC -_Discrimination of protein secondary structure at BMM (ICRF / London)
  • GOR - Garnier, Osgoodthorpe and Robson (GOR) secondary structure prediction method (at SBDS)
  • nnPredict - University of California at San Francisco (UCSF)
  • PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from EMBL
  • PREDATOR - Protein secondary structure prediction from single sequence at EMBL (Argos' group)
  • PSA - BioMolecular Engineering Research Center (BMERC) / Boston
  • SSPRED - Protein secondary structure prediction from aligned sequences at EMBL (Argos' group)

• Tertiary structure
  • Swiss-Model - an automated knowledge-based protein modelling server
  • Swiss-PdbViewer - a program to analyse and superimpose protein 3D structures

• Transmembrane regions detection
  • SOSUI - Prediction of transmembrane regions from TUAT (Tokyo Univ. of Agriculture & Tech.)
  • TMpred - Prediction of transmembrane regions and protein orientation at ISREC
  • TMAP - Transmembrane detection based on multiple sequence alignment at EMBL
  • DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method at Stockholm

• Alignment
  • Binary
    • SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
  • Multiple
    • CLUSTALW - at the EBI
    • MSA - at Washington University
    • Align query - at EERIE
    • Multalin - at I.N.R.A.

    • AMAS - Analyse Multiply Aligned Sequences
    • Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building).

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Last modified 10/June/1997 by AB

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