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Nucleic Acids Research 2005 33(Web Server Issue):W274-W276; doi:10.1093/nar/gki493
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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

SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs

Saikat Chakrabarti, A. Prem Anand1, Nitin Bhardwaj2, Ganesan Pugalenthi and R. Sowdhamini*

National Centre for Biological Sciences (NCBS) Bangalore 560065, India 1International Institute of Information Technology (MSIT) Hyderabad 500 019, India 2Department of Chemical Engineering, Indian Institute of Technology Mumbai 400 076, India

*To whom correspondence should be addressed. Tel: +91 80 23636421/8, ext. 4240/1; Fax: +91 80 23636665; Email: mini{at}ncbs.res.in

Received February 14, 2005. Revised April 25, 2005. Accepted April 25, 2005.

Establishment of similarities between proteins is very important for the study of the relationship between sequence, structure and function and for the analysis of evolutionary relationships. Motif-based search methods play a crucial role in establishing the connections between proteins that are particularly useful for distant relationships. This paper reports SCANMOT, a web-based server that searches for similarities between proteins by simultaneous matching of multiple motifs. SCANMOT searches for similar sequences in entire sequence databases using multiple conserved regions and utilizes inter-motif spacing as restraints. The SCANMOT server is available via http://www.ncbs.res.in/~faculty/mini/scanmot/scanmot.html.

Present addresses: Saikat Chakrabarti, Computational Biology Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA

Prem Anand, Institute for Genomics and Bioinformatics, Graz University of Technology, Graz-8010, Austria

Nitin Bhardwaj, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA


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