Skip Navigation



Bioinformatics Advance Access published online on March 22, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm097
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/10/1181    most recent
btm097v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Mudunuri, S. B.
Right arrow Articles by Nagarajaram, H. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Mudunuri, S. B.
Right arrow Articles by Nagarajaram, H. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
A. Merkel and N. Gemmell
Detecting short tandem repeats from genome data: opening the software black box
Brief Bioinform, September 1, 2008; 9(5): 355 - 366.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.