RT Journal
A1 Allen, Jonathan E.
A1 Pertea, Mihaela
A1 Salzberg, Steven L.
T1 Computational Gene Prediction Using Multiple Sources of Evidence
JF Genome Research 
JO Genome Research 
YR 2004 
FD January 01 
VO 14 
IS 1 
SP 142 
OP 148 
DO 10.1101/gr.1562804 
UL http://genome.cshlp.org/content/14/1/142.abstract 
AB This article describes a computational method to construct gene models by using evidence generated from a diverse set of sources, including those typical of a genome annotation pipeline. The program, called Combiner, takes as input a genomic sequence and the locations of gene predictions from ab initio gene finders, protein sequence alignments, expressed sequence tag and cDNA alignments, splice site predictions, and other evidence. Three different algorithms for combining evidence in the Combiner were implemented and tested on 1783 confirmed genes in Arabidopsis thaliana. Our results show that combining gene prediction evidence consistently outperforms even the best individual gene finder and, in some cases, can produce dramatic improvements in sensitivity and specificity.