Identifying multiple alignment regions satisfying simple formulas and patterns.

Nikola Stojanovic; Ken Dewar

doi:10.1093/bioinformatics/bth196

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Identifying multiple alignment regions satisfying simple formulas and patterns.

Nikola Stojanovic·Ken Dewar

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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 PPARgamma 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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Algorithms Artificial Intelligence Conserved Sequence Gene Frequency PPAR gamma Pattern Recognition, Automated Sequence Alignment Sequence Analysis, DNA Sequence Homology, Nucleic Acid Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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Nikola Stojanovic, Ken Dewar. 2004-03-25. Identifying multiple alignment regions satisfying simple formulas and patterns.. https://doi.org/10.1093/bioinformatics%2Fbth196

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