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Bioinformatics Advance Access published online on December 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti224
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received November 10, 2004
Revised December 6, 2004
Accepted December 13, 2004

Applications note

SITEBLAST - rapid and sensitive local alignment of genomic sequences employing motif anchors

Morris Michael 1, Christoph Dieterich 1*, and Martin Vingron 1

1 Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, D-14195 Berlin, Germany

* To whom correspondence should be addressed.
Christoph Dieterich, E-mail: christoph.dieterich{at}molgen.mpg.de


  Abstract

Motivation: Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications of local alignment algorithms (e.g. phylogenetic footprinting) would benefit from including prior knowledge (e.g. binding site motifs) in the alignment building process.

Results: We introduce predefined sequence patterns as anchor points into a heuristic local alignment strategy. We extended the BLASTZ program for this purpose. A set of seed patterns is either given as consensus sequences in IUPAC code or position-weight-matrices (PWMs). Phylogenetic footprinting of promoter regions is one of many potential applications for the SITEBLAST software.

Availability: The source code is freely available to the academic community from http://corg.molgen.mpg.de/software.


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