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PMID: 15571632 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

prot4EST: translating expressed sequence tags from neglected genomes.

BMC bioinformatics ·Vol. 5 ·2004-11-30 ·Pages 187

Wasmuth JD, Blaxter ML

Abstract

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. 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. 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.

MeSH Terms
Animals Arabidopsis/genetics Artificial Intelligence Base Composition/genetics Benchmarking/methods Caenorhabditis elegans/genetics Codon/genetics DNA, Helminth/genetics DNA, Plant/genetics Databases, Genetic Expressed Sequence Tags/metabolism Genome Genome, Bacterial Genome, Plant Humans Protein Biosynthesis/genetics Software Software Design Spirurida/genetics
Chemicals
Codon DNA, Helminth DNA, Plant
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Wasmuth James D
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK. [email protected]
Blaxter Mark L
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Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-5-187
Email
[email protected]
Published
2004-11-30
Epub
2004-00-30
Pages
187
Language
English
Region
England
NLM ID
100965194
PMCID
PMC543579
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2105-5-187 PMC Full Text View journal details
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