Nucleic Acids Research Advance Access originally published online on May 24, 2008
Nucleic Acids Research 2008 36(Web Server issue):W25-W29; doi:10.1093/nar/gkn320
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W25-W29
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
1College of Life Sciences, University of Dundee, Dundee DD1 5EH, 2EMBL-European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, 3Departments of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford OX1 3QX, 4The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and 5Biomatters Ltd, Level 6 FAI Building, 220 Queen St, Auckland 1001, New Zealand
*To whom correspondence should be addressed. Tel: +01382 385860; Fax: +01382 385764; Email: geoff{at}compbio.dundee.ac.uk
Received January 31, 2008. Revised April 27, 2008. Accepted May 7, 2008.
SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance. This combination gives good sensitivity and selectivity that outperforms PSI-BLAST in domain-searching benchmarks. Although computationally expensive, SCANPS exploits onchip parallelism (MMX and SSE2 instructions on Intel chips) as well as MPI parallelism to give acceptable turnround times even for large databases. A web server developed to run SCANPS searches is now available at http://www.compbio.dundee.ac.uk/www-scanps. The server interface allows a range of different protein sequence databases to be searched including the SCOP database of protein domains. The server provides the user with regularly updated versions of the main protein sequence databases and is backed up by significant computing resources which ensure that searches are performed rapidly. For SCOP searches, the results may be viewed in a new tree-based representation that reflects the structure of the SCOP hierarchy; this aids the user in placing each hit in the context of its SCOP classification and understanding its relationship to other domains in SCOP.