ArticleBMC genomics2009
ESTPiper--a web-based analysis pipeline for expressed sequence tags.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.BMC bioinformatics · 2015Article
- Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.Physiology and molecular biology of plants : an international journal of functional plant biology · 2014Article
- Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum.BMC genomics · 2013Article
- Bio301: A Web-Based EST Annotation Pipeline That Facilitates Functional Comparison Studies.ISRN bioinformatics · 2012Article
- Comparative analysis of putative pathogenesis-related gene expression in two Rhizoctonia solani pathosystems.Current genetics · 2011Article
- Gene discovery in Triatoma infestans.Parasites & vectors · 2011Article
- PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.BMC research notes · 2011Article
- Analysis of a botryllid enriched-full-length cDNA library: insight into the evolution of spliced leader trans-splicing in tunicates.Development genes and evolution · 2011Article
- The mining of toxin-like polypeptides from EST database by single residue distribution analysis.BMC genomics · 2011Article
- Developmental decoupling of alternative phenotypes: insights from the transcriptomes of horn-polyphenic beetles.Evolution; international journal of organic evolution · 2011Article
- Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera.BMC genomics · 2010Article
- A survey of well conserved families of C2H2 zinc-finger genes in Daphnia.BMC genomics · 2010Article
- EST and microarray analysis of horn development in Onthophagus beetles.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components.
resultsThe intuitive web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation, analysis of gene ontology (GO), and microarray oligonucleotide probe design. Each step is modularized. Therefore, a user can execute them separately or together in batch mode. In addition, the user has control over the parameters used by the underlying programs. Extensive documentation of ESTPiper's functionality is embedded throughout the web site to facilitate understanding of the required input and interpretation of the computational results. The user can also download intermediate results and port files to separate programs for further analysis. In addition, our server provides a time-stamped description of the run history for reproducibility. The pipeline can also be installed locally, allowing researchers to modify ESTPiper to suit their own needs.
conclusionESTPiper streamlines the typical process of EST analysis. The pipeline was initially designed in part to support the Daphnia pulex cDNA sequencing project. A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ to now support projects of all size. The software is also freely available from the authors for local installations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.