ArticleNucleic acids research2007
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- CerealESTDb: A Comprehensive Resource for Abiotic Stress-Responsive Annotated ESTs With Predicted Genes, Gene Ontology, and Metabolic Pathways in Major Cereal Crops.Frontiers in genetics · 2022Article
- Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.PloS one · 2015Article
- Transcriptome profiling of the fifth-stage larvae of Angiostrongylus cantonensis by next-generation sequencing.Parasitology research · 2013Article
- RCDA: a highly sensitive and specific alternatively spliced transcript assembly tool featuring upstream consecutive exon structures.Genomics · 2012Article
- The transcriptome analysis of Strongyloides stercoralis L3i larvae reveals targets for intervention in a neglected disease.PLoS neglected tropical diseases · 2012Article
- TranSeqAnnotator: large-scale analysis of transcriptomic data.BMC bioinformatics · 2012Article
- FastAnnotator--an efficient transcript annotation web tool.BMC genomics · 2012Article
- Association between polymorphisms in GRIK2 gene and obsessive-compulsive disorder: a family-based study.CNS neuroscience & therapeutics · 2011Article
- Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies.Parasites & vectors · 2011Review
- The mining of toxin-like polypeptides from EST database by single residue distribution analysis.BMC genomics · 2011Article
- First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2010Article
- Quail Genomics: a knowledgebase for Northern bobwhite.BMC bioinformatics · 2010Article
- Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera.BMC genomics · 2010Article
- A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing.Nucleic acids research · 2010Article
- From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite.Physiological genomics · 2010Article
- Differences in transcription between free-living and CO2-activated third-stage larvae of Haemonchus contortus.BMC genomics · 2010Article
- SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read.BMC bioinformatics · 2010Article
- Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases.BMC genomics · 2009Article
- An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host.Molecular & cellular proteomics : MCP · 2009Article
- EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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