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Open Access Highly Accessed Methodology article

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

Alexander Churbanov*, Mark Pauley, Daniel Quest and Hesham Ali

Author Affiliations

Department of Computer Science, College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182-0116, USA

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BMC Bioinformatics 2005, 6:261  doi:10.1186/1471-2105-6-261

Published: 21 October 2005



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.