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Nucleic Acids Research 2005 33(Web Server Issue):W284-W288; doi:10.1093/nar/gki418
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

FFAS03: a server for profile–profile sequence alignments

Lukasz Jaroszewski, Leszek Rychlewski1, Zhanwen Li, Weizhong Li and Adam Godzik*

Bioinformatics Program, The Burnham Institute 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA 1BioInfoBank Institute ul. Limanowskiego 24 A, 60-744 Poznan, Poland

*To whom correspondence should be addressed. Tel: +1 858 646 3168; Fax: +1 858 713 9925; Email: adam{at}burnham.org

Received February 17, 2005. Revised March 21, 2005. Accepted March 21, 2005.

The FFAS03 server provides a web interface to the third generation of the profile–profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232–241]. Profile–profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. As a result, they enable detection of remote homologies beyond the reach of other methods. FFAS, initially developed in 2000, is consistently one of the best ranked fold prediction methods in the CAFASP and LiveBench competitions. It is also used by several fold-recognition consensus methods and meta-servers. The FFAS03 server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins from PDB, COG, PFAM and SCOP. The profile databases used by the server are automatically updated with the latest structural and sequence information. The server provides access to the alignment analysis, multiple alignment, and comparative modeling tools. Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at http://ffas.burnham.org.

Present address: Lukasz Jaroszewski, Joint Center for Structural Genomics, UCSD, La Jolla, CA 92093, USA


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