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Bioinformatics Vol. 19 no. 18 2003
pages 2486-2488
© 2003 Oxford University Press

Applications Note

PRIMEX: rapid identification of oligonucleotide matches in whole genomes

Matej Lexa 1,* and Giorgio Valle 2

1 Laboratory of Functional Genomics and Proteomics, Masaryk University Brno, Kotlarska 2, 61137 Brno, Czech Republic and 2 CRIBI Biotechnology Center, University of Padova, via U.Bassi, 58/b, 35131 Padova, Italy

Received on March 24, 2003 ; revised on May 30, 2003 ; accepted on July 1, 2003

Summary: PRIMEX (PRImer Match EXtractor) can detect oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries from client software and returns matches rapidly. We find it faster and more sensitive than currently available tools.

Availability: Running applications and source code have been made available at http://bioinformatics.cribi.unipd.it/primex

Contact: m-lexa{at}sci.muni.cz

* To whom correspondence should be addressed at CRIBI Biotechnology Center, University of Padova, via U.Bassi, 58/b, 35131 Padova, Italy.


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