ExPASy Proteomics tools

[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]

Similarity searches

BLAST and WU-BLAST - Interfaces to various versions of the Basic Local Alignment Search Tool BLAST Network Service on ExPASy BLAST at EMBnet-CH/SIB (Switzerland) BLAST at NCBI WU-BLAST at Bork's group in EMBL (Heidelberg) WU-BLAST and BLAST at the EBI (Hinxton) BLAST at PBIL (Lyon) Bic ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator [At DKFZ or at Weizmann] MPsrch - Smith/Waterman sequence comparison at EBI 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 - 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; [at EBI / ExPASy ] 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 O-GalNAc (mucin type) glycosylation sites in mammalian proteins NetNGlyc - Prediction of N-glycosylation sites in human 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 - Prediction of tyrosine sulfation sites SUMOplot - Prediction of SUMO protein attachment 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 - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.) Compute pI/Mw - 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 2ZIP - Prediction of Leucine Zippers 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 - 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 Three To One - Tool to convert a three-letter coded amino acid sequence to single letter code 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 - 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 University of Dundee 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 - 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 - A program to display, analyse and superimpose protein 3D structures

Sequence alignment
Binary
SIM + LALNVIEW - 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

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