Using multiple alignments to improve gene prediction.
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.
Gross
Samuel S
SS
Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA. ssgross@cs.stanford.edu
Brent
Michael R
MR
D000818:Animals; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D016208:Databases, Factual; D004331:Drosophila melanogaster / Q000235:genetics; D005091:Exons / Q000235:genetics*; D016678:Genome; D006801:Humans; D008957:Models, Genetic; D011237:Predictive Value of Tests; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data; D012984:Software
D004247:DNA