ExPASy tools menu

Sequence analysis tools

• 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
• Swiss-Model - an automated knowledge-based protein modelling server

• AACompIdent - Identify a protein by its amino acid composition
• AACompSim - Compare the amino acid composition of a SWISS-PROT entry with all other entries
• GuessProt - Get the SWISS-PROT proteins closest to a given pI and Mw.
• Compute pI/Mw - Compute the theoretical pI and Mw from a SWISS-PROT entry or for a user sequence

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

• Similarity searches
  • BLAST - Interface to Basic Local Alignment Search Tool: at NCBI - at EPFL
  • BLITZ - EBI's ultra-fast protein database searches using MPsearch
  • Bic - Weizmann's ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator
  • BioSCAN - Biological Sequence Comparative Analysis at U. North Carolina
  • 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
  • Bipartite NLS Locator - Detection of bipartite nuclear localization sequences

• Primary sequence analysis
  • ProtParam - Physico-chemical parameters of a protein sequence (composition, extinction coefficient, etc.)
  • SAPS - Statistical analysis of protein sequences
  • 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
  • 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
  • PHD - (ProteinPredict) EMBL / Heidelberg
  • AntheProt - Institute of Biology and Chemistry of Proteins (IBCP) / Lyon
  • nnPredict - University of California at San Francisco (UCSF)
  • BCM PSSP - Baylor College of Medecine
  • PSA - BioMolecular Engineering Research Center (BMERC) / Boston
  • GOR - Garnier, Osgoodthorpe and Robson (GOR) secondary structure prediction method (at SBDS)

• Transmembrane regions detection
  • TMpred - Prediction of transmembrane regions and protein orientation at ISREC
  • TMAP - Transmembrane detection based on multiple sequence alignment at EMBL

• Alignment
  • Binary
    • SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
  • Multiple
    • MSA - at Washington University
    • Align query - at EERIE
    • Multalin - at IBCP

• Do you really want to see the results?

Last modified 16/Feb/1996 by AB

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