Nucleic Acids Research Advance Access originally published online on June 1, 2007
Nucleic Acids Research 2007 35(Web Server issue):W143-W147; doi:10.1093/nar/gkm378
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W143-W147
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
1Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia, 2Department of Veterinary Sciences, The University of Melbourne, Werribee, VIC 3030, Australia and 3Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119260
*To whom correspondence should be addressed. Tel: +61 2 9850 6262; Fax: +61 2 9850 8313; Email: shoba.ranganathan{at}mq.edu.au
Received January 28, 2007. Revised March 30, 2007. Accepted April 30, 2007.
The analysis of expressed sequence tag (EST) datasets offers a rapid and cost-effective approach to elucidate the transcriptome of an organism, but requiring several computational methods for assembly and annotation. ESTExplorer is a comprehensive workflow system for EST data management and analysis. The pipeline uses a ‘distributed control approach’ in which the most appropriate bioinformatics tools are implemented over different dedicated processors. Species-specific repeat masking and conceptual translation are in-built. ESTExplorer accepts a set of ESTs in FASTA format which can be analysed using programs selected by the user. After pre-processing and assembly, the dataset is annotated at the nucleotide and protein levels, following conceptual translation. Users may optionally provide ESTExplorer with assembled contigs for annotation purposes. Functionally annotated contigs/ESTs can be analysed individually. The overall outputs are gene ontologies, protein functional identifications in terms of mapping to protein domains and metabolic pathways. ESTExplorer has been applied successfully to annotate large EST datasets from parasitic nematodes and to identify novel genes as potential targets for parasite intervention. ESTExplorer runs on a Linux cluster and is freely available for the academic community at http://estexplorer.biolinfo.org.
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