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

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, micro-exons and partial gene structure predictions that span across several genomic clones. We present a mRNA/DNA homology...

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Bibliographic Details
Published in:BMC bioinformatics 2005-10, Vol.6 (1), p.261-261, Article 261
Main Authors: Churbanov, Alexander, Pauley, Mark, Quest, Daniel, Ali, Hesham
Format: Article
Language:English
Subjects:
Algorithms
Clone Cells - chemistry
DNA - chemistry
Methodology
Predictive Value of Tests
RNA, Messenger - chemistry
Sequence Alignment
Sequence Homology, Nucleic Acid
Software
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Summary: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, micro-exons and partial gene structure predictions that span across several genomic clones. 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 noisy Genie learning set simulating ESTs. GIGOgene shows a higher quality of gene structure prediction for mRNA/DNA spliced alignment when compared to other available tools.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-6-261