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Bioinformatics Advance Access originally published online on March 22, 2004
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Bioinformatics 20(12) © Oxford University Press 2004; all rights reserved.

Applications Note

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments

Mikita Suyama {dagger}, David Torrents {dagger} and Peer Bork *

Biocomputing, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69012 Heidelberg, Germany

Received on January 5, 2004; accepted on January 29, 2004
Advance Access Publication March 22, 2004

Summary: BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide query sequence with any genomic region of interest, BLAST2GENE processes all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment. The results are provided in text and PostScript formats to allow an automatic and visual evaluation of the respective region.

Availability: The program is available upon request from the authors. A web server of BLAST2GENE is maintained at http://www.bork.embl.de/blast2gene

Contact: bork{at}embl.de

* To whom correspondence should be addressed.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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