PRIMEX: rapid identification of oligonucleotide matches in whole genomes.
CONCLUSIONS
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.


BACKGROUND
Running applications and source code have been made available at http://bioinformatics.cribi.unipd.it/primex
Lexa
Matej
M
Laboratory of Functional Genomics and Proteomics, Masaryk University Brno, Kotlarska 2, 61137 Brno, Czech Republic. m-lexa@sci.muni.cz
Valle
Giorgio
G
D000465:Algorithms; D016678:Genome; D009841:Oligonucleotides / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D009841:Oligonucleotides