EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance.docVIP

BMC Bioinformatics BioMedCentral Research article Open Access EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance Thomas Schou Larsen*1,2 and Anders Krogh1,3 Address: 1Center for Biological Sequence Analysis BioCentrum, Technical University of Denmark Building 208, 2800 Lyngby, Denmark, 2Present address: Novozymes A/S, Novo Alle, 1B1.01,2800 Bagsvaerd, Denmark and 3Present address: The Bioinformatics Centre, University of Copenhagen Universitetsparken 15, 2100 Copenhagen, Denmark Email: Thomas Schou Larsen* - thsl@; Anders Krogh - krogh@binf.ku.dk * Corresponding author Published: 3 June 2003 Received: 25 November 2002 Accepted: 3 June 2003 BMC Bioinformatics 2003, 4:21 This article is available from: /1471-2105/4/21 ? 2003 Larsen and Krogh; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the articles original URL. computational gene findingstatistical significancehidden Markov modelshort open reading framesautomated genome annotation Abstract Background: Contrary to other areas of sequence analysis, a measure of statistical significance of a putative gene has not been devised to help in discriminating real genes from the masses of random Open Reading Frames (ORFs) in prokaryotic genomes. Therefore, many genomes have too many short ORFs annotated as genes. Results: In this paper, we present a new automated gene-finding method, EasyGene, which estimates the statistical significance of a predicted gene. The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Using extensions of similarities in Swiss-Prot, a high quality training set of genes is automatically extracted from the genome and used to estimate the HMM. Putative genes are then scored with the HMM, and based on score