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

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

SUBMITTER: Nadershahi A 

PROVIDER: S-EPMC375524 | biostudies-literature | 2004 Feb

REPOSITORIES: biostudies-literature