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
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
start of a gene (the presumptive promoter), or all hits within the first
of genes. Output is tab-delimitted text with a variety of useful result
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
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
primarily as a research tool for the bench scientist. There are brief
user documentation pages.
- Jim Thomas
James H. Thomas
Department of Genome Sciences
University of Washington [Only registered users see links. ]