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

Alexander Churbanov, Mark A Pauley, Daniel Quest, Hesham H Ali

Research output: Contribution to journalArticle

6 Citations (Scopus)

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, micro-exons 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. Conclusions: GIGOgene shows a higher quality of gene structure prediction for mRNA/DNA spliced alignment when compared to other available tools.

Original languageEnglish (US)
Article number261
JournalBMC bioinformatics
Volume6
DOIs
StatePublished - Oct 21 2005

Fingerprint

Structure Prediction
Messenger RNA
Homology
DNA
Genes
Gene
Prediction
Exons
Alignment
Learning
Partial
Prediction Interval
Interval Graphs
Expressed Sequence Tags
Bioinformatics
Computational Biology
Clone
Specificity
Genomics
Annotation

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

A method of precise mRNA/DNA homology-based gene structure prediction. / Churbanov, Alexander; Pauley, Mark A; Quest, Daniel; Ali, Hesham H.

In: BMC bioinformatics, Vol. 6, 261, 21.10.2005.

Research output: Contribution to journalArticle

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