genBlastG: extending BLAST to be a high performance gene finder

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 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. htm l Contact: chenn@ sfu. ca