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          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents



ID: 272173.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors
Authors:Michael, Morris; Dieterich, Christoph; Vingron, Martin
Language:English
Date of Publication (YYYY-MM-DD):2005-01-01
Title of Journal:Bioinformatics
Volume:21
Issue / Number:9
Start Page:2093
End Page:2094
Copyright:© 2006 Oxford University Press
Review Status:not specified
Audience:Experts Only
Abstract / Description: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.
Comment of the Author/Creator:The source code is freely available to the academic community from http://corg.molgen.mpg.de/software
External Publication Status:published
Document Type:Article
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
Identifiers:DOI:10.1093/bioinformatics/bti224
ISSN:1367-4803
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