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|
|Date of Publication (YYYY-MM-DD):||2005-01-01|
|Title of Journal:||Bioinformatics|
|Issue / Number:||9|
|Copyright:||© 2006 Oxford University Press|
|Review Status:||not specified|
|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|
|Communicated by:||Martin Vingron|
|Affiliations:||MPI für molekulare Genetik|
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