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


BACKGROUND
The source code is freely available to the academic community from http://corg.molgen.mpg.de/software
Michael
Morris
M
Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
Dieterich
Christoph
C
Vingron
Martin
M
D000465:Algorithms; D020816:Amino Acid Motifs; D002874:Chromosome Mapping / Q000379:methods*; D016384:Consensus Sequence; D004282:Documentation / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software