Document Type

Article

Publication Date

10-21-2005

Publication Title

BMC Bioinformatics

Volume

6

Issue

261

First Page

1

Last Page

13

Abstract

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 noisy Genie learning set simulating ESTs.

Conclusion: GIGOgene shows a higher quality of gene structure prediction for mRNA/DNA spliced alignment when compared to other available tools.

Comments

© 2005 Churbanov et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).

doi:10.1186/1471-2105-6-261

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