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

Nagaraj, Shivashankar H., Gasser, Robin B. and Ranganathan, Shoba (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics, 8 1: 6-21. doi:10.1093/bib/bbl015


Author Nagaraj, Shivashankar H.
Gasser, Robin B.
Ranganathan, Shoba
Title A hitchhiker's guide to expressed sequence tag (EST) analysis
Journal name Briefings in Bioinformatics   Check publisher's open access policy
ISSN 1467-5463
1477-4054
Publication date 2007-01
Sub-type Editorial
DOI 10.1093/bib/bbl015
Volume 8
Issue 1
Start page 6
End page 21
Total pages 16
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
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.
Keyword Expressed sequence tags
Sequence assembly and clustering
Database similarity searches
Functional annotation
Conceptual translation
Transcriptome analysis
Q-Index Code CX
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Editorial
Collection: Institute for Molecular Bioscience - Publications
 
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Created: Wed, 21 Mar 2012, 09:53:19 EST by Susan Allen on behalf of Institute for Molecular Bioscience