A hitchhiker's guide to expressed sequence tag (EST) analysis

A hitchhiker's guide to expressed sequence tag (EST) analysis Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive computational strategies have been developed to organize and analyse both small- and large-scale EST data for gene discovery, transcript and single nucleotide polymorphism analysis as well as functional annotation of putative gene products.We provide an overview of the significance of ESTs in the genomic era, their properties and the applications of ESTs. Methods adopted for each step of EST analysis by various research groups have been compared. Challenges that lie ahead in organizing and analysing the ever increasing EST data have also been identified.The most appropriate software tools for EST pre-processing, clustering and assembly, database matching and functional annotation have been compiled (available online from http://biolinfo.org/EST). We propose a road map for EST analysis to accelerate the effective analyses of EST data sets. An investigation of EST analysis platforms reveals that they all terminate prior to downstream functional annotation including gene ontologies, motif/pattern analysis and pathway mapping. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Briefings in Bioinformatics Oxford University Press

A hitchhiker's guide to expressed sequence tag (EST) analysis

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Publisher
Oxford University Press
Copyright
© Published by Oxford University Press.
ISSN
1467-5463
eISSN
1477-4054
D.O.I.
10.1093/bib/bbl015
Publisher site
See Article on Publisher Site

Abstract

Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive computational strategies have been developed to organize and analyse both small- and large-scale EST data for gene discovery, transcript and single nucleotide polymorphism analysis as well as functional annotation of putative gene products.We provide an overview of the significance of ESTs in the genomic era, their properties and the applications of ESTs. Methods adopted for each step of EST analysis by various research groups have been compared. Challenges that lie ahead in organizing and analysing the ever increasing EST data have also been identified.The most appropriate software tools for EST pre-processing, clustering and assembly, database matching and functional annotation have been compiled (available online from http://biolinfo.org/EST). We propose a road map for EST analysis to accelerate the effective analyses of EST data sets. An investigation of EST analysis platforms reveals that they all terminate prior to downstream functional annotation including gene ontologies, motif/pattern analysis and pathway mapping.

Journal

Briefings in BioinformaticsOxford University Press

Published: Jan 23, 2007

Keywords: expressed sequence tags sequence assembly and clustering database similarity searches functional annotation conceptual translation transcriptome analysis

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