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

Item Type:	Article
Title:	SITEBLAST - rapid and sensitive local alignment of genomic sequences employing motif anchors
Creators Name:	Michael, M. and Dieterich, C. and Vingron, M.
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. AVAILABILITY: The source code is freely available to the academic community from http://corg.molgen.mpg.de/software
Keywords:	Algorithms, Amino Acid Motifs, Chromosome Mapping, Consensus Sequence, Documentation, Sequence Alignment, DNA Sequence Analysis, Software
Source:	Bioinformatics
ISSN:	1367-4803
Publisher:	Oxford University Press
Volume:	21
Number:	9
Page Range:	2093-2094
Date:	2005
Official Publication:	https://doi.org/10.1093/bioinformatics/bti224
PubMed:	View item in PubMed

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