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Briefings in Bioinformatics Advance Access published online on May 23, 2006
Briefings in Bioinformatics, doi:10.1093/bib/bbl015
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 24, 2006

Original Papers

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

Shivashankar H. Nagaraj, Robin B. Gasser, and Shoba Ranganathan *

* To whom correspondence should be addressed.
Shoba Ranganathan, E-mail: shoba{at}els.mq.edu.au


  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.

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

Shivashankar H. Nagaraj is an international Macquarie University scholarship graduate student at the Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney. He is using comparative genomics to identify novel therapeutic gene targets.

Robin B. Gasser is a Professor and Reader in Veterinary Parasitology, Department of Veterinary Science, The University of Melbourne, working on generating gender-specific EST libraries of parasitic nematodes affecting livestock animals.

Shoba Ranganathan is a Chair Professor of Bioinformatics at Macquarie University and Adjunct Professor, National University of Singapore. Her research work focuses on computational structural biology and comparative genome sequence analysis.


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