ExPASy Proteomics tools

[Protein identification and characterization] [DNA -> Protein] [Similarity searches] [Pattern and profile searches] [Primary structure analysis] [Secondary structure prediction] [Tertiary structure] [Transmembrane regions detection] [Sequence alignment]

Similarity searches

BLAST and WU-BLAST - Interfaces to various versions of the Basic Local Alignment Search Tool BLAST at NCBI WU-BLAST and BLAST 2.0 at EMBnet-CH (Lausanne) WU-BLAST at Bork's group in EMBL (Heidelberg) WU-BLAST and BLAST at the EBI (Hinxton) BLAST at PBIL (Lyon) BLITZ - EBI's ultra-fast protein database searches using MPsearch Bic ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator [At EBI, DKFZ or at Weizmann] BioSCAN - Biological Sequence Comparative Analysis at U. North Carolina DeCypher II - 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) PropSearch - Search for structural homologs using a 'properties' approach SAMBA - Systolic Accelerator for Molecular Biological Applications Scanps - Similarity searches using Barton's algorithm

Pattern and profile searches

ScanProsite - Scan a sequence against PROSITE or a pattern against SWISS-PROT and TrEMBL ProfileScan - Scan a sequence against protein profile databases (including PROSITE) Frame-ProfileScan - Scan a short DNA sequence against protein profile databases (including PROSITE) Pfam HMM search to scan a sequence against the Pfam protein families db [At Washington University or at Sanger Centre] FPAT - Regular expression searches in protein databases PRATT - Interactively generates conserved patterns from a series of unaligned proteins PPSEARCH - Scans a sequence against PROSITE from EBI (allows a graphical output) PROSITE scan at PBIL - Scans a sequence against PROSITE (allows mismatches)

Primary structure analysis

ProtParam - Physico-chemical parameters of a protein sequence (composition, pI, extinction coefficient, etc.) MW, pI, Titration curve - Also computes pI, composition and allows to see a titration curve 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 signal peptide cleavage sites ChloroP - Chloroplast Transit Peptide Prediction NetOGlyc - Prediction of type O-glycosylation sites in mammalian proteins NetPicoRNA - Prediction of protease cleavage sites in picornavial proteins 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 HLA_Bind - HLA Peptide Binding Prediction PEST - Identification of "PEST" regions REPRO - Recognition of protein sequence repeats at EMBL 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 - Tool to represent a protein fragment as an helical wheel RandSeq - Random protein sequence generator

Secondary structure prediction

AGADIR - An algorithm to predict the helical content of peptides BCM PSSP - Baylor College of Medicine DSC - Discrimination of protein secondary structure at BMM (ICRF / London) 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) 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 or multiple sequences at EMBL (Argos' group) PSA - BioMolecular Engineering Research Center (BMERC) / Boston SOPM (Geourjon et Deléage, 1994) SOPMA (Geourjon et Deléage, 1995) 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 CPHmodels (Sowhat) - Prediction of distance constraints from a protein sequence

Transmembrane regions detection

DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method at Stockholm University HMMTOP - Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences SOSUI - Prediction of transmembrane regions from TUAT (Tokyo Univ. of Agriculture & Tech.) TMAP - Transmembrane detection based on multiple sequence alignment at EMBL TMHMM - Prediction of transmembrane helices in proteins at CBS (Technical University of Denmark) TMpred - Prediction of transmembrane regions and protein orientation at EMBnet-CH TopPred 2 - Topology prediction of membrane proteins at Stockholm University

Sequence alignment
Binary
SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW
Multiple
CLUSTALW [At EBI or at PBIL] MSA - at Washington University ALIGN - at Genestream (IGH) Multalin [At INRA or at PBIL] 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