J Comput Biol. 2006 Mar;13(2):379-93.

Using multiple alignments to improve gene prediction.

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Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA. ssgross@cs.stanford.edu

Abstract

The multiple species de novo gene prediction problem can be stated as follows: given an alignment of genomic sequences from two or more organisms, predict the location and structure of all protein-coding genes in one or more of the sequences. Here, we present a new system, N-SCAN (a.k.a. TWINSCAN 3.0), for addressing this problem. N-SCAN can model the phylogenetic relationships between the aligned genome sequences, context dependent substitution rates, and insertions and deletions. An implementation of N-SCAN was created and used to generate predictions for the entire human genome and the genome of the fruit fly Drosophila melanogaster. Analyses of the predictions reveal that N-SCAN's accuracy in both human and fly exceeds that of all previously published whole-genome de novo gene predictors.

PMID:: 16597247; [PubMed - indexed for MEDLINE]

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