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

被引：22

作者：

Lee, Byungwook ^{[1
,2
]}

Hong, Taehui ^{[1
]}

Byun, Sang Jin ^{[3
]}

Woo, Taeha ^{[1
]}

Choi, Yoon Jeong ^{[1
]}

机构：

[1] KRIBB, Korean Bioinformat Ctr, Taejon 305817, South Korea

[2] Korea Adv Inst Sci & Technol, Dept BioSyst, Taejon 305701, South Korea

[3] Bioneer, Bioinformat Team, Taejon 306220, South Korea

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

关键词：

D O I：

10.1093/nar/gkm369

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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/.

引用

页码：W159 / W162

页数：4

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