We have developed, over the years, an extensive collection of software tools, most of which are either targeted toward the access and display of the databases mentioned above, or can be used to analyze protein sequences and proteomics data originating from 2D-PAGE and mass spectrometry experiments. These latter tools can all be accessed from ExPASy (http://www.expasy.org/tools/
Database query, display and navigation
A variety of query options are available from the home pages of each of the ExPASy databases. These options allow the users to display and retrieve specified subsets of the database. For example, from the home page of SWISS-PROT and TrEMBL, different query forms allow searching by description, accession number, author, citation or by full text search. To complement these options, we have also implemented an SRS (11
) server that allows complex searches on any fields of the combination of SWISS-PROT and TrEMBL databases. PROSITE, ENZYME and SWISS-2DPAGE can also be queried using SRS.
The original flat file format of all ExPASy databases is based on different line types, where a two-letter line code defines the information contained on the rest of that line (e.g. for SWISS-PROT: see the user manual, http://www.expasy.org/sprot/userman.html
). This format is easy to parse by computer programs, but not necessarily easy to read for human users. In order to provide a more verbose and user-friendly view of the database entries, we provide for each database, on ExPASy, a ‘nice’ hypertext view, e.g. NiceProt for SWISS-PROT and TrEMBL entries. An example for an entry in the NiceProt view can be seen at http://www.expasy.org/cgi-bin/niceprot.pl?P57727
, or in Figure . The figure shows parts of that entry in order to illustrate the easy navigation between information contained in the entry itself, the corresponding documentation, remote databases, and the submission forms or results of sequence alignment or other ExPASy analysis tools. Similar views are available for PROSITE (NiceSite and NiceDoc), ENZYME (NiceZyme) and SWISS-2DPAGE (Nice2Dpage).
Figure 1 The NiceProt view of a SWISS-PROT entry presents its contents in a user-friendly view. Links are provided to >70 databases, a user manual and other documents. NiceProt is also integrated with tools provided on ExPASy and other servers. Excerpts (more ...)
) is an automated sequence alerting system which allows users to obtain new SWISS-PROT entries relevant to their field(s) of interest. Keyword-based and sequence/pattern-based requests are possible. Every time a weekly SWISS-PROT release is performed, all new database entries matching the user-specified search keywords or patterns or the entries showing sequence similarities to the user-specified sequence are automatically sent to the user by email.
Sequence analysis tools
- BLAST (12) provides very fast similarity searches of a protein sequence against a protein or nucleotide database. The ExPASy BLAST service is maintained in collaboration with the Swiss EMBnet node on dedicated hardware. The native output of BLAST is extended with several original features (Fig. ).
- ScanProsite (13) scans a sequence against all the patterns, profiles and rules in PROSITE or scans a pattern, profile or rule against all sequences in SWISS-PROT, TrEMBL and/or PDB.
- SWISS-MODEL (14,15) is an automated knowledge-based protein modelling server. It is able to build models for the 3D structure of proteins whose sequence is closely related to that of proteins with known 3D structure.
- ProtParam calculates physico-chemical parameters of a protein sequence such as the amino acid composition, the pl, the atomic composition, the extinction coefficient, etc.
- ProtScale computes and represents the profile produced by any amino acid scale on a selected protein. Some 50 predefined scales are available, such as the Doolittle and Kyte hydrophobicity scale.
- RandSeq generates a random protein sequence, based on a user-specified amino acid composition and sequence length.
- Sulfinator (16) predicts tyrosine sulfation sites within protein sequences.
- Translate translates a nucleotide sequence into a protein in six reading frames.
- AACompIdent (17) identifies a protein by its amino acid composition.
- AACompSim (17) finds for a given SWISS-PROT entry, the database entries which have the most similar amino acid composition.
- Compute pI/MW (18) computes the theoretical isoelectric point (pI) and molecular weight (MW) from a SWISS-PROT or TrEMBL entry or for a user sequence.
- FindMod (19) predicts potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified SWISS-PROT entry or from a user-entered sequence. Mass differences are used to better characterize the protein of interest.
- FindPept (20) identifies peptides resulting from unspecific cleavage of proteins by their experimental masses, taking into account artefactual chemical modifications, post-translational modifications and protease autolytic cleavage.
- GlycanMass calculates the mass of an oligosaccharide structure.
- GlycoMod (21) predicts possible oligosaccharide structures that occur on proteins from their experimentally determined masses. This is done by comparing the mass of a potential glycan to a list of pre-computed masses of glycan compositions.
- PeptideCutter predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.
- PeptideMass (22) calculates the theoretical masses of peptides generated by the chemical or enzymatic cleavage of proteins so as to assist in the interpretation of peptide mass fingerprinting.
- PeptIdent, TagIdent, MultiIdent (23–25), these three related programs identify proteins using a variety of experimental information such as the pI, the MW, the amino acid composition, partial sequence tags and peptide mass fingerprinting data.
A very important feature of the ExPASy proteomics tools (such as PeptIdent, TagIdent, MultiIdent, PeptideMass, FindPept or FindMod) is that, when performing their computations and predictions, they use the annotations relevant to post-translational modifications and processing, as well as splice variants documented in the SWISS-PROT feature tables.
These tools are all listed on a page on ExPASy (http://www.expasy.org/tools/
) that also offers links to many other useful programs for the analysis of protein sequences available elsewhere on the web. We notably have links to the tools provided by our colleagues from the bioinformatics group at ISREC (http://www.isrec.isb-sib.ch
) and the Swiss EMBnet node (http://www.ch.embnet.org
) in Lausanne. They have developed a BLAST similarity search server, TMpred (to predict transmembrane regions) and interfaces to the SAPS (Statistical Analysis of Protein Sequences), COILS (prediction of coiled coil regions), Clustal and T-Coffee (multiple sequence alignment) programs.