Paper Info
Title
In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches.
Abstract
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.
Year
DOI
Venue
2008
10.1186/1471-2105-9-S1-S10
BMC Bioinformatics
Keywords
Field
DocType
drug targeting,algorithms,expressed sequence tag,sterilization,ion channel,database search,enzyme,cost effectiveness,data analysis,bioinformatics,transcription factors,molecular biology,microarrays,expressed sequence tags,comparative genomics,kyoto encyclopedia of genes and genomes
Trichostrongylus vitrinus,ORDER STRONGYLIDA,Trichostrongylus,Annotation,Expressed sequence tag,Computer science,Bioinformatics,Genetics,Workflow,Database,DNA microarray,In silico
Journal
Volume
Issue
ISSN
9
S-1
1471-2105
Citations 
PageRank 
References 
40
0.60
10
Authors
4
Name
Order
Citations
PageRank
Shivashankar H. Nagaraj11035.03
Robin B. Gasser2816.46
Alasdair J. Nisbet3400.60
Shoba Ranganathan468936.60