new elegans, briggsae, drosophila DNA motif searcher

A new on-line program for searching the C. elegans, C. briggsae, or
D. melanogaster genomes for matches to a set of DNA sequences is
now available at:
[Only registered users see links. ]

It accepts as input a set (1 or more) of short DNA sequences and
searches
the genome sequence for probabilistic matches to them. It doesn't allow
gaps but otherwise uses a sophisticated search algorithm, including
accounting for background nucleotide frequencies of the genome as a
whole. You can set hit threshholds or a best hit count.

There are options for showing where search hits are located with respect
to predicted gene starts, ends, and exons/introns. This permits you to
easily find, for example, all hits that reside within some distance of
the
start of a gene (the presumptive promoter), or all hits within the first
intron
of genes. Output is tab-delimitted text with a variety of useful result
fields
so that it can be imported to a spreadsheet for post-search processing.

The program is intended to find matches to a set of defined
transcription
factor
binding sites, but should be useful for any ungapped set of related DNA
sequences. The program is written by a biologist for biologists and is
intended
primarily as a research tool for the bench scientist. There are brief
but
clear
user documentation pages.

- Jim Thomas

James H. Thomas
Professor
Department of Genome Sciences
University of Washington
[Only registered users see links. ]


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