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

Mikita Suyama; David Torrents; Peer Bork

doi:10.1093/bioinformatics/bth172

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

Bioinformatics. 2004 Aug 12;20(12):1968-70. doi: 10.1093/bioinformatics/bth172. Epub 2004 Mar 22.

Authors

Mikita Suyama¹, David Torrents, Peer Bork

Affiliation

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

PMID: 15037510
DOI: 10.1093/bioinformatics/bth172

Abstract

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

MeSH terms

Algorithms*
Chromosome Mapping / methods*
Gene Dosage*
Genetic Variation
Information Storage and Retrieval / methods
Internet
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Sequence Analysis, Protein / methods
Software*
User-Computer Interface*