new DNA motif searcher on-line

James H. Thomas jht at
Wed Sep 24 09:04:37 EST 2003

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

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
Department of Genome Sciences
University of Washington
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