genBlastG: using BLAST searches to build homologous gene models

Motivation: BLAST users frequently expect to obtain homologous genes with certain similarity to their query genes. But what they get from BLAST searches are often collections of local alignments called high-scoring segment pairs (HSPs). On the other hand, most homology-based gene finders have been built using computation-intensive algorithms, without taking full advantage of BLAST searches that have been perfected over the last decades. Results: Here we report an efficient algorithm, genBlastG that directly uses the HSPs reported by BLAST to define high-quality gene models. Availability: http://genome.sfu.ca/genblast/download.html Contact: chenn@sfu.ca Supplementary information: Supplementary data are available at Bioinformatics online.