Expressed Sequence Tags (ESTs) pp 221-239

Part of the Methods in Molecular Biology book series (MIMB, volume 533) | Cite as

Obtaining Accurate Translations from Expressed Sequence Tags

  • James Wasmuth
  • Mark Blaxter
Protocol

Abstract

The genomes of an increasing number of species are being investigated through the 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 describe how this integrated approach goes a long way to overcoming the deficit in training data.

Key words

Expressed sequence tags ESTs protein translations, simulated transcriptomes 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • James Wasmuth
    • 1
    • 2
  • Mark Blaxter
    • 1
  1. 1.Institute of Evolutionary Biology, University of EdinburghEdinburghUK
  2. 2.Program for Molecular Structure and Function, Hospital for Sick ChildrenOntarioCanada

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