Integrating genomic homology into gene structure prediction

Ian F Korf, Paul Flicek, Daniel Duan, Michael R. Brent

Research output: Contribution to journalArticle

327 Scopus citations

Abstract

TWINSCAN is a new gene-structure prediction system that directly extends the probability model of GENSCAN, allowing it to exploit homology between two related genomes. Separate probability models are used for conservation in exons, introns, splice sites, and UTRs, reflecting the differences among their patterns of evolutionary conservation. TWINSCAN is specifically designed for the analysis of high-throughput genomic sequences containing an unknown number of genes. In experiments on high-throughput mouse sequences, using homologous sequences from the human genome, TWINSCAN shows notable improvement over GENSCAN in exon sensitivity and specificity and dramatic improvement in exact gene sensitivity and specificity. This improvement can be attributed entirely to modeling the patterns of evolutionary conservation in genomic sequence.

Original languageEnglish (US)
JournalBioinformatics
Volume17
Issue numberSUPPL. 1
StatePublished - 2001
Externally publishedYes

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

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    Korf, I. F., Flicek, P., Duan, D., & Brent, M. R. (2001). Integrating genomic homology into gene structure prediction. Bioinformatics, 17(SUPPL. 1).