title: ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences.
abstract: 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/.
authors.affiliation: Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea.
authors.forename: Byungwook
authors.initials: B
authors.lastname: Lee
authors.forename: Taehui
authors.initials: T
authors.lastname: Hong
authors.forename: Sang Jin
authors.initials: SJ
authors.lastname: Byun
authors.forename: Taeha
authors.initials: T
authors.lastname: Woo
authors.forename: Yoon Jeong
authors.initials: YJ
authors.lastname: Choi
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003199:Computer Systems; D018076:DNA, Complementary / Q000378:metabolism*; D003628:Database Management Systems; D004926:Escherichia coli / Q000235:genetics*; D005786:Gene Expression Regulation; D005796:Genes; D006801:Humans; D020407:Internet; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D018076:DNA, Complementary