Title
Estexplorer: An Expressed Sequence Tag (Est) Assembly And Annotation Platform
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 http://estexplorer.biolinfo.org.
Year
DOI
Venue
2007
10.1093/nar/gkm378
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Ontology (information science),Expressed sequence tag,Annotation,Protein domain,Biology,Contig,Genomics,Computational biology,Bioinformatics,FASTA format,Genetics,Workflow
Journal
35
Issue
ISSN
Citations 
Web-Server
0305-1048
8
PageRank 
References 
Authors
0.79
15
4
Name
Order
Citations
PageRank
Shivashankar H. Nagaraj11035.03
Nandan Deshpande230932.76
Robin B. Gasser3816.46
Shoba Ranganathan468936.60