Comparison of computational methods for identifying translation initiation sites in EST data.docVIP

BMC Bioinformatics BioMedCentral Research article Open Access Comparison of computational methods for identifying translation initiation sites in EST data Afshin Nadershahi1, Scott C Fahrenkrug2 and Lynda BM Ellis*3 Address: 1College of Biological Science, University of Minnesota, St. Paul, MN 55108 USA, 2Department of Animal Science, University of Minnesota, St. Paul, MN 55108 USA and 3Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455 USA Email: Afshin Nadershahi - nade0043@; Scott C Fahrenkrug - fahre001@; Lynda BM Ellis* - lynda@ * Corresponding author Published: 16 February 2004 Received: 13 August 2003 Accepted: 16 February 2004 BMC Bioinformatics 2004, 5:14 This article is available from: /1471-2105/5/14 ? 2004 Nadershahi et al; 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. Abstract Background: Expressed Sequence Tag (EST) sequences are generally single-strand, single-pass sequences, only 200–600 nucleotides long, contain errors resulting in frame shifts, and represent different parts of their parent cDNA. If the cDNAs contain translation initiation sites, they may be suitable for functional genomics studies. We have compared five methods to predict translation initiation sites in EST data: first-ATG, ESTScan, Diogenes, Netstart, and ATGpr. Results: A dataset of 100 EST sequences, 50 with and 50 without, translation initiation sites, was created. Based on analysis of this dataset, ATGpr is found to be the most accurate for predicting the presence versus absence of translation initiation sites. With a maximum accuracy of 76%, ATGpr more accurately predicts the position or absence of translation initiation sites than NetStart (57%) or Diogenes (50%). ATGpr similarly e