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Bioinformatics Advance Access published online on March 22, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm097
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

IMEx: Imperfect Microsatellite Extractor

Suresh B. Mudunuri and Hampapathalu A. Nagarajaram *

Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), ECIL Road, Nacharam, Hyderabad 500 076, India

*To whom correspondence should be addressed. Hampapathalu A. Nagarajaram, E-mail: han{at}cdfd.org.in, suresh{at}cdfd.org.in


  Abstract

Motivation: Microsatellites, also known as Simple Sequence Repeats, are the tandem repeats of nucleotide motifs of the size 1-6bp found in every genome known so far. Their importance of Microsatellites or Simple Sequence Repeats (SSR's) in genomes is well known. Microsatellites are associated with various disease genes, have been used as molecular markers in linkage analysis and DNA fingerprinting studies, and also seem to play an important role in the genome evolution. How microsatellites take ‘birth’, ‘evolve’ and ‘die’ have not been clearly understood although some recent studies reveal the role of point mutations in the genesis and evolution of microsatellites. Therefore, it is of importance to study study distribution, enrichment and polymorphism of microsatellites in the genomes of interest. For this, the prerequisite is the availability of a computational tool for extraction of microsatellites (perfect as well imperfect) and their related information from whole genome sequences. Examination of available tools revealed certain lacunae and prompted us to develop a new tool.

Results: In order to efficiently screen genome sequences for microsatellites (perfect as well as imperfect) we developed a new tool this communication, we present the details of a new tool called IMEx (Imperfect Microsatellite Extractor). IMEx uses simple string matching algorithm with sliding window approach to screen DNA sequences for microsatellites and reports the motif, copy number, genomic location, nearby genes, mutational events and many other features useful for in-depth studies. IMEx is more sensitive, efficient, and useful than the available widely used tools. IMEx is available in the form of a stand-alone program as well as in the form of a web-server.

Availability: World Wide Web server has also been created and is available for free access at http://203.197.254.154/IMEX/ or http://www.cdfd.org.in/imex

Associate Editor: Dr. Alex Bateman

Received on December 15, 2006; revised on February 26, 2007; accepted on March 7, 2007

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