Bioinformatics Vol. 17 no. 90001 2001
Pages S140-S148
© 2001 Oxford University Press
Integrating genomic homology into gene structure prediction
1 Department of Computer Science, Washington
University, Campus Box 1045, St. Louis, MO, 63130, USA
2 Department of Biomedical Engineering,
Washington University, Campus Box 1097, St. Louis, MO, 63130, USA
Received on February 6, 2001
; revised on April 2, 2001
; accepted on April 2, 2001
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.
Contact: ikorf{at}cs.wustl.edu; pflicek{at}cs.wustl.edu; duan{at}cs.wustl.edu; brent{at}cs.wustl.edu
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