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Nucleic Acids Research Advance Access published online on May 25, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm369
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences

Byungwook Lee1,2, Taehui Hong1, Sang Jin Byun3, Taeha Woo1 and Yoon Jeong Choi1,*

1Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea, 2Department of BioSystems, KAIST, Daejeon 305-701, Korea and 3Bioinformatics team, Bioneer, 49-3 Munpyeong-dong, Daedeok-gu, Daejeon 306-220, Korea

*To whom correspondence should be addressed. Tel: +82 42 879 8521; Fax: +82-42-879-8519; Email: yjchoi{at}kribb.re.kr

Received January 31, 2007. Revised April 10, 2007. Accepted April 26, 2007.

We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass accepts a FASTA-formatted EST file and its quality file as inputs, and it then executes a back-end EST analysis pipeline consisting of three consecutive steps. The first is cleansing the input EST sequences. The second is clustering and assembling the cleansed EST sequences using d2_cluster and CAP3 programs and producing putative transcripts. From the CAP3 output, ESTpass detects chimeric EST sequences which are confirmed through comparison with the nr database. The last step is annotating the putative transcript sequences using RefSeq, InterPro, GO and KEGG gene databases according to user-specified options. The major advantages of ESTpass are the integration of cleansing and annotating processes, rigorous chimeric EST detection, exhaustive annotation, and email reporting to inform the user about the progress and to send the analysis results. The ESTpass results include three reports (summary, cleansing and annotation) and download function, as well as graphic statistics. They can be retrieved and downloaded using a standard web browser. The server is available at http://estpass.kobic.re.kr/.


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