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. 2003 Jul 1;31(13):3784-8.
doi: 10.1093/nar/gkg563.

ExPASy: The proteomics server for in-depth protein knowledge and analysis

Elisabeth Gasteiger  1 , Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D Appel, Amos Bairoch
Affiliations

ExPASy: The proteomics server for in-depth protein knowledge and analysis

Elisabeth Gasteiger et al. Nucleic Acids Res. .

Abstract

The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.

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Figures

Figure 1
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 of the view of a sample entry are presented in this figure. A BLASTP similarity search against SWISS-PROT/TrEMBL/TrEMBLnew can be performed with a single click (button 1) on a very fast server (median request time: 6 s). BLAST parameters can also be adjusted by accessing the BLAST page (link 2), which provides a choice of BLASTP or TBLASTN over a choice of databases and subsections. The result page (inset 3) combines a BLASTP search with a motif search in the PROSITE profiles and Pfam HMM domain databases and displays a graphical overview of the matching regions both on the query and on the hit. From there, it is possible to browse matching entries, including splice variants; to rerun a BLAST search after masking regions that match PROSITE or Pfam domains in order to find weaker similarities in other regions and to perform multiple alignments of selected hit sequences.
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References

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