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Bioinformatics Advance Access published online on October 14, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp587
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ABWGAT: Anchor Based Whole Genome Analysis Tool.

Sarbashis Das 1, Anchal Vishnoi 1 and Alok Bhattacharya 1,2,*

1 Center for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Delhi 110067
2 School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.

*To whom correspondence should be addressed. Prof. Alok Bhattacharya, E-mail: lok.bhattacharya{at}gmail.com


  Abstract

Summary: Large numbers of genomes are being sequenced regularly and the rate will go up in future due to availability of new genome sequencing techniques. In order to understand genotype to phenotype relationships it is necessary to identify sequence variations at the genomic level. Alignment of a pair of genomes and parsing the alignment data is an accepted approach for identification of variations. Though there are a number of tools available for whole genome alignment none of these allows automatic parsing of the alignment and identification of different kinds of genomic variants with high degree of sensitivity. Here we present a simple web based interface for whole genome comparison named ABWGAT (Anchor Based Whole Genome Analysis Tool) that is simple to use. The output is a list of variations such as SNVs, INDELs, Repeat expansion and Inversion.

Availability: The web server is freely available to non-commercial users at the following address: http://abwgc.jnu.ac.in/~sarba/

Contact: dsarbashis{at}gmail.com

Supplementary Information: Supplementary data are available at http://abwgc.jnu.ac.in/~sarba/cgi-bin/abwgc_retrival.cgi using job id 524, 526 and 528.

Associate Editor: Prof. Alfonso Valencia

Received on July 21, 2009; revised on September 25, 2009; accepted on October 8, 2009

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