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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
genBlastG: using BLAST searches to build homologous gene models
Rong She1, Jeffrey Shih-Chieh Chu, Bora Uyar
1School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada V5A 0A1.
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
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