Integrating genomic homology into gene structure prediction

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

Research output: Contribution to journalArticle

323 Citations (Scopus)

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

Fingerprint

Structure Prediction
Genomics
Homology
Genes
Gene
Conservation
Exons
Probability Model
High Throughput
Specificity
Untranslated Regions
Sensitivity and Specificity
Genome
Human Genome
Sequence Homology
Introns
Throughput
Mouse
Unknown
Modeling

ASJC Scopus subject areas

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

Cite this

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

Integrating genomic homology into gene structure prediction. / Korf, Ian F; Flicek, Paul; Duan, Daniel; Brent, Michael R.

In: Bioinformatics, Vol. 17, No. SUPPL. 1, 2001.

Research output: Contribution to journalArticle

Korf, IF, Flicek, P, Duan, D & Brent, MR 2001, 'Integrating genomic homology into gene structure prediction', Bioinformatics, vol. 17, no. SUPPL. 1.
Korf, Ian F ; Flicek, Paul ; Duan, Daniel ; Brent, Michael R. / Integrating genomic homology into gene structure prediction. In: Bioinformatics. 2001 ; Vol. 17, No. SUPPL. 1.
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