SCANMOT: Searching for Similar Sequences Using a Simultaneous Scan of Multiple Sequence Motifs

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Jun 28

PMID 15980468

Citations 8

Authors

Saikat Chakrabarti

A Prem Anand

Nitin Bhardwaj

Ganesan Pugalenthi

R Sowdhamini

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

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Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.

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MegaMotifBase: a database of structural motifs in protein families and superfamilies.

Pugalenthi G, Suganthan P, Sowdhamini R, Chakrabarti S Nucleic Acids Res. 2007; 36(Database issue):D218-21.

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Recent trends in remote homology detection: an Indian Medley.

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