prot4EST: translating expressed sequence tags from neglected genomes.
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.
Wasmuth
James D
JD
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK. james.wasmuth@ed.ac.uk
Blaxter
Mark L
ML
D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D001185:Artificial Intelligence; D001482:Base Composition / Q000235:genetics; D019985:Benchmarking / Q000379:methods; D017173:Caenorhabditis elegans / Q000235:genetics*; D003062:Codon / Q000235:genetics; D018509:DNA, Helminth / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags / Q000378:metabolism*; D016678:Genome; D016680:Genome, Bacterial; D018745:Genome, Plant; D006801:Humans; D014176:Protein Biosynthesis / Q000235:genetics*; D012984:Software; D012985:Software Design; D017174:Spirurida / Q000235:genetics
D003062:Codon; D018509:DNA, Helminth; D018744:DNA, Plant