prot4EST: translating expressed sequence tags from neglected genomes.
BMC Bioinformatics
; 5: 187, 2004 Nov 30.
Article
en En
| MEDLINE
| ID: mdl-15571632
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.
Texto completo:
1
Colección:
01-internacional
Asunto principal:
Biosíntesis de Proteínas
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Programas Informáticos
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Genoma
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Caenorhabditis elegans
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Arabidopsis
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Etiquetas de Secuencia Expresada
Límite:
Animals
/
Humans
Idioma:
En
Revista:
BMC Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2004
Tipo del documento:
Article
País de afiliación:
Reino Unido