Overview
SHOPS (SHow OPeron Structures) was developed to analyze the genomic operon context for any group of proteins selected on the basis of a set of sequence or domain identifiers. It uses genome annotations of all available fully sequenced prokaryotes to create a scaled graphical overview of the genomic context around the proteins of interest.
At the most basic level, SHOPS can be used to display the genomic neighborhood of a protein of interest, annotated with currently available functional data on neighboring genes, as well as domain structures. When supplied with a protein family, either a set of manually selected proteins or a known domain or COG, it can also be used to search for evolutionary conserved operon structures. SHOPS accepts identifiers from a wide range of domain databases, including InterPro, Pfam, SMART, PROSITE, PRODOM, TIGRFAMs, Superfamily, PRINTS, PIR, Gene3D and PANTHER. Finally, the operon contexts can also be used to assign new functions to unknown proteins.

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News
version 2.1
ExPASy
  • As of the first of November 2005, SHOPS has been integrated into the sequence hub of ExPASy.
version 2.0
  • Major rewrite of code base, lots of new features! (see Changelog)
  • Added 30 new prokaryotes to the database
version 1.1
  • Minor update: added ~90 new organisms to the database
version 1.0
  • SHOPS is born...

References

To cite shops please use: Bioinformatics. 2004 Nov 1;20(16):2644-55.

References to data sets and software used in SHOPS can be found here.

Questions or comments may be addressed to bioinformatics -at- azu.nl .

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