ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform

Nagaraj, Shivashankar H., Deshpande, Nandan, Gasser, Robin B. and Ranganathan, Shoba (2007) ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. Nucleic Acids Research, 35 W143-W147. doi:10.1093/nar/gkm378

Author Nagaraj, Shivashankar H.
Deshpande, Nandan
Gasser, Robin B.
Ranganathan, Shoba
Title ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2007-07
Sub-type Article (original research)
DOI 10.1093/nar/gkm378
Open Access Status DOI
Volume 35
Start page W143
End page W147
Total pages 5
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Abstract 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
Keyword Suppressive-subtractive hybridisation
Microarray analysis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes First published online: 1 June 2007. Issue Web Server issue

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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Created: Wed, 21 Mar 2012, 09:51:36 EST by Susan Allen on behalf of Institute for Molecular Bioscience