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Nucleic Acids Research 2004 32(Web Server Issue):W649-W653; doi:10.1093/nar/gkh455
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval

Jeff Reneker1,2, Chi-Ren Shyu1,2,*, Peiyu Zeng5, Joseph C. Polacco3 and Walter Gassmann4

1 Department of Computer Science, 2 Department of Health Management and Informatics, 3 Department of Agriculture Biochemistry and 4 Department of Plant Pathology, University of Missouri, Columbia, MO 65211, USA and 5 Department of Plant Science, University of Rhode Island, Kingston, RI, 02881, USA

* To whom correspondence should be addressed. Tel: +1 573 882 3842; Fax: +1 573 882 3813; Email: shyuc{at}missouri.edu

Received February 15, 2004; Revised April 15, 2004; Accepted April 23, 2004

We have developed a web server for the life sciences community to use to search for short repeats of DNA sequence of length between 3 and 10 000 bases within multiple species. This search employs a unique and fast hash function approach. Our system also applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. Furthermore, we have incorporated a part of the Gene Ontology database into our information retrieval algorithms to broaden the coverage of the search. Our web server and tutorial can be found at http://acmes.rnet.missouri.edu.

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