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

Abstract

We have developed a web server for the life sciences community to use to search for short repeats of DNA sequence of length between 3and 10000 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 befound at http://acmes.rnet.missouri.edu. © Oxford University Press 2004; all rights reserved.