TOOLS: Repeat Finder

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Science  16 Nov 2001:
Vol. 294, Issue 5546, pp. 1423
DOI: 10.1126/science.294.5546.1423d

The genomes of humans and many other species have been sequenced by now, but figuring out what the sequence means is still mostly unexplored territory, says cell biologist Betsey Dyer of Wheaton College in Norton, Massachusetts. And just about anyone can “slice off a little problem and go to work on it.”

That's why Dyer, computer science colleague Mark LeBlanc, and a team of undergraduates have developed a set of tools for analyzing potential regulatory sequences of genes. One tool scans chromosomes 3 and 10 of Caenorhabditis elegans and pinpoints inverted repeats: short stretches of DNA that contain a sequence and its complementary sequence and that may play a role in gene regulation. Another tool finds repeats associated with the Krebs cycle. And the Motif Lexicon scans the C. elegans genome for sequences as short as four bases long—snippets that big-name search tools like BLAST may have a hard time finding, Dyer says.

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