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BMCBI
2005

A method of precise mRNA/DNA homology-based gene structure prediction

11 years 1 months ago
A method of precise mRNA/DNA homology-based gene structure prediction
Background: Accurate and automatic gene finding and structural prediction is a common problem in bioinformatics, and applications need to be capable of handling non-canonical splice sites, microexons and partial gene structure predictions that span across several genomic clones. Results: We present a mRNA/DNA homology based gene structure prediction tool, GIGOgene. We use a new affine gap penalty splice-enhanced global alignment algorithm running in linear memory for a high quality annotation of splice sites. Our tool includes a novel algorithm to assemble partial gene structure predictions using interval graphs. GIGOgene exhibited a sensitivity of 99.08% and a specificity of 99.98% on the Genie learning set, and demonstrated a higher quality of gene structural prediction when compared to Sim4, est2genome, Spidey, Galahad and BLAT, including when genes contained micro-exons and non-canonical splice sites. GIGOgene showed an acceptable loss of prediction quality when confronted with a ...
Alexander G. Churbanov, Mark Pauley, Daniel Quest,
Added 15 Dec 2010
Updated 15 Dec 2010
Type Journal
Year 2005
Where BMCBI
Authors Alexander G. Churbanov, Mark Pauley, Daniel Quest, Hesham H. Ali
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