Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 13, Issue 2, Pages 379-393Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2006.13.379
Keywords
gene prediction; genome annotation; comparative genomics; phylogenetic models
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Funding
- NHGRI NIH HHS [HG02278] Funding Source: Medline
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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.
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