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Bioinformatics Advance Access published online on March 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth196
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 31, 2003
Revised February 12, 2004
Accepted February 13, 2004

Applications note

Identifying multiple alignment regions satisfying simple formulas and patterns

Nikola Stojanovic 1* Ken Dewar 2

1 Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, 76019, USA
2 Department of Human Genetics, McGill University, QC, H3A 1A4, Canada; Genome Quebec Innovation Centre, Montreal, QC, H3A 1A4, Canada

* To whom correspondence should be addressed. E-mail: nick{at}cse.uta.edu.


  Abstract

Motivation: When studying multiple alignments of genomic sequences one frequently aims to locate and count regions which satisfy a set of constraints. These regions may be putatively functional, but researchers may also be interested in quantifying the frequency of occurrences of certain patterns.

Results: We have developed a program that applies simple formulas and pattern specifications to multiple alignments, reporting the positions and counts of conforming regions. As an example, we have navigated a 15-species alignment of the CAV2-CAV1 region and outlined some findings regarding PPAR{gamma} binding sites.

Availability: Our software and the accompanying documentation can be obtained at no charge by contacting the authors. It can also be accessed at http://ranger.uta.edu/~nick/compgen.


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