Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Software

prot4EST: Translating Expressed Sequence Tags from neglected genomes

James D Wasmuth* and Mark L Blaxter

Author Affiliations

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK

For all author emails, please log on.

BMC Bioinformatics 2004, 5:187  doi:10.1186/1471-2105-5-187

Published: 30 November 2004

Abstract

Background

The genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects.

Results

As part of our ongoing EST programs investigating these "neglected" genomes, we have developed a polypeptide prediction pipeline, prot4EST. It incorporates freely available software to produce final translations that are more accurate than those derived from any single method. We show that this integrated approach goes a long way to overcoming the deficit in training data.

Conclusions

prot4EST provides a portable EST translation solution and can be usefully applied to >95% of EST projects to improve downstream annotation. It is freely available from http://www.nematodes.org/PartiGene webcite.