In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): Comparison of the automated ESTExplorer workflow platform with conventional database searches

Nagaraj, Shivashankar H., Gasser, Robin B., Nisbet, Alasdair J. and Ranganathan, Shoba (2008). In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): Comparison of the automated ESTExplorer workflow platform with conventional database searches. In: Shoba Ranganathan, Michael Gribskov and Tin Wee Tan, Proceedings: from Sixth International Conference on Bioinformatics (InCoB2007). Asia Pacific Bioinformatics Network (APBioNet) Sixth International Conference on Bioinformatics (InCoB2007), Hong Kong, (S10.1-S10.17). 27-30 August 2007. doi:10.1186/1471-2105-9-S1-S10


Author Nagaraj, Shivashankar H.
Gasser, Robin B.
Nisbet, Alasdair J.
Ranganathan, Shoba
Title of paper In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): Comparison of the automated ESTExplorer workflow platform with conventional database searches
Formatted title
In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): Comparison of the automated ESTExplorer workflow platform with conventional database searches
Conference name Asia Pacific Bioinformatics Network (APBioNet) Sixth International Conference on Bioinformatics (InCoB2007)
Conference location Hong Kong
Conference dates 27-30 August 2007
Proceedings title Proceedings: from Sixth International Conference on Bioinformatics (InCoB2007)   Check publisher's open access policy
Journal name BMC Bioinformatics   Check publisher's open access policy
Place of Publication London, United Kingdom
Publisher BioMed Central
Publication Year 2008
Sub-type Fully published paper
DOI 10.1186/1471-2105-9-S1-S10
Open Access Status DOI
ISSN 1471-2105
Editor Shoba Ranganathan
Michael Gribskov
Tin Wee Tan
Volume 9
Issue Suppl 1
Start page S10.1
End page S10.17
Total pages 17
Language eng
Formatted Abstract/Summary
Background: The analysis of expressed sequence tags (EST) offers a rapid and cost effective approach to elucidate the transcriptome of an organism, but requires several computational methods for assembly and annotation. Researchers frequently analyse each step manually, which is laborious and time consuming. We have recently developed ESTExplorer, a semi-automated computational workflow system, in order to achieve the rapid analysis of EST datasets. In this study, we evaluated EST data analysis for the parasitic nematode Trichostrongylus vitrinus (order Strongylida) using ESTExplorer, compared with database matching alone.
Results: We functionally annotated 1776 ESTs obtained via suppressive-subtractive hybridisation from T. vitrinus, an important parasitic trichostrongylid of small ruminants. Cluster and comparative genomic analyses of the transcripts using ESTExplorer indicated that 290 (41%) sequences had homologues in Caenorhabditis elegans, 329 (42%) in parasitic nematodes, 202 (28%) in organisms other than nematodes, and 218 (31%) had no significant match to any sequence in the current databases. Of the C. elegans homologues, 90 were associated with 'non-wildtype' double-stranded RNA interference (RNAi) phenotypes, including embryonic lethality, maternal sterility, sterile progeny, larval arrest and slow growth. We could functionally classify 267 (38%) sequences using the Gene Ontologies (GO) and establish pathway associations for 230 (33%) sequences using the Kyoto Encyclopedia of Genes and Genomes (KEGG). Further examination of this EST dataset revealed a number of signalling molecules, proteases, protease inhibitors, enzymes, ion channels and immune-related genes. In addition, we identified 40 putative secreted proteins that could represent potential candidates for developing novel anthelmintics or vaccines. We further compared the automated EST sequence annotations, using ESTExplorer, with database search results for individual T. vitrinus ESTs. ESTExplorer reliably and rapidly annotated 301 ESTs, with pathway and GO information, eliminating 60 low quality hits from database searches.
Conclusion: We evaluated the efficacy of ESTExplorer in analysing EST data, and demonstrate that computational tools can be used to accelerate the process of gene discovery in EST sequencing projects. The present study has elucidated sets of relatively conserved and potentially novel genes for biological investigation, and the annotated EST set provides further insight into the molecular biology of T. vitrinus, towards the identification of novel drug targets.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article # S10

Document type: Conference Paper
Collection: Institute for Molecular Bioscience - Publications
 
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Created: Wed, 21 Mar 2012, 09:49:41 EST by Susan Allen on behalf of Institute for Molecular Bioscience