• AMAS - Analyse Multiply Aligned Sequences
  [A program to analyse multiple alignments of protein sequences; allowing identification of functional residues by comparison of sub-groups of sequences]
  
• CombSearch
  [An experimental unified interface to query several protein identification tools accessible on the web]
  
• Compute pI/Mw tool
  [Allows the computation of the theoretical isoelectric point and molecular weight for a list of Swiss-Prot and/or TrEMBL entries or for a user entered sequence]
  
• ExPASy Proteomics tools
  [Various tolls for protein identification and characterization]
  
• Fasta - Proteine Database Query
  [Provides sequence similarity and homology searching against nucleotide and protein databases using the Fasta programs]
  
• FindMod tool
  [A tool that can predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides]
  
• FingerPRINTScan Submission Form
  [Search against FingerPRINTScan with a protein query sequence to identify the closest matching PRINTS sequence motif fingerprints in a protein sequence]
  
• Helmholtz Network for Bioinformatics
  [A variety of programs & databases for nucleic acid & protein analysis providing prediction and analysis of regulatory regions in eukaryotic genomic sequences]
  
• InterProScan Sequence Search
  [This form allows you to query your sequence against InterPro]
  
• Pedant-Proteine extraction, description and analysis tool
  [A software system for completely automatic and exhaustive analysis of protein sequence sets from individual sequences to complete genomes]
  
• PeptIdent
  [Allows the identification of proteins using pI, Mw & peptide mass fingerprinting data compared with peptides calculated in Swiss-Prot/TrEMBL databases]
  
• PIR Database Information
  [An integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery]
  
• PoPS: Prediction of Protease Specificity
  [A program that allows users to model and profile protease specificity and predict substrate cleavage]
  
• PPSearch Submission Form
  [Query sequence search for protein motifs, rapidly compare against all patterns of PROSITE pattern database & determine function of uncharacterised protein]
  
• ProtParam tool
  [A tool allowing the computation of various physical & chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence]
  
• ProtScale
  [Allows you to compute and represent the profile produced by any amino acid scale on a selected protein]
  
• Radar Submission Form
  [Rapid Automatic Detection and Alignment of Repeats in protein sequences. Identifies short composition biased as well as gapped approximate repeats...]
  
• SAPS - Statistical Analysis of Protein Sequences
  [Methods and algorithms for statistical analysis of protein sequences]
  
• ScanPS Submission Form
  [A program for comparing a protein sequence to a database of protein sequences implementing the full Smith-Waterman style searching]
  
• SignalP V1.1 World Wide Web Prediction Server
  [Predicts the presence & location of signal peptide cleavage sites in amino acid sequences from different organisms: prokaryotes and eukaryotes]
  
• The PredictProtein server
  [A service for sequence analysis, and structure prediction]
  
• TMHMM Server v. 2.0
  [Prediction of transmembrane helices in proteins]
  
• TMpred - Prediction of Transmembrane Regions and Orientation
  [Prediction of membrane-spanning regions & their orientation based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins]
  

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