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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 174.
Published online Apr 21, 2009. doi:  10.1186/1471-2164-10-174
PMCID: PMC2676306
ESTPiper – a web-based analysis pipeline for expressed sequence tags
Reviewed by Zuojian Tang,1 Jeong-Hyeon Choi,1 Chris Hemmerich,1 Ankita Sarangi,1 John K Colbourne,corresponding author1 and Qunfeng Dongcorresponding author1
1The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
corresponding authorCorresponding author.
Zuojian Tang: tangz/at/cgb.indiana.edu; Jeong-Hyeon Choi: jeochoi/at/cgb.indiana.edu; Chris Hemmerich: chemmeri/at/cgb.indiana.edu; Ankita Sarangi: sarangia/at/indiana.edu; John K Colbourne: jcolbour/at/cgb.indiana.edu; Qunfeng Dong: qfdong/at/cgb.indiana.edu
Received September 26, 2008; Accepted April 21, 2009.
Abstract
Background
EST 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.
Results
The 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.
Conclusion
ESTPiper 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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