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

Michael, Morris; Dieterich, Christoph; Vingron, Martin

doi:10.1093/bioinformatics/bti224

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

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Dieterich, Christoph
Max Planck Society;

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Vingron, Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Michael, M., Dieterich, C., & Vingron, M. (2005). SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors. Bioinformatics, 21(9), 2093-2094. doi:10.1093/bioinformatics/bti224.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-8745-E

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. Phylogenetic footprinting of promoter regions is one of many potential applications for the SITEBLAST software.