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PMID: 12409467 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

PipeOnline 2.0: automated EST processing and functional data sorting.

Nucleic acids research ·Vol. 30 ·No. 21 ·2002-11-01 ·Pages 4761-9

Ayoubi P, Jin X, Leite S, Liu X, Martajaja J, Abduraham A, Wan Q, Yan W, Misawa E, Prade RA

Abstract

Expressed sequence tags (ESTs) are generated and deposited in the public domain, as redundant, unannotated, single-pass reactions, with virtually no biological content. PipeOnline automatically analyses and transforms large collections of raw DNA-sequence data from chromatograms or FASTA files by calling the quality of bases, screening and removing vector sequences, assembling and rewriting consensus sequences of redundant input files into a unigene EST data set and finally through translation, amino acid sequence similarity searches, annotation of public databases and functional data. PipeOnline generates an annotated database, retaining the processed unigene sequence, clone/file history, alignments with similar sequences, and proposed functional classification, if available. Functional annotation is automatic and based on a novel method that relies on homology of amino acid sequence multiplicity within GenBank records. Records are examined through a function ordered browser or keyword queries with automated export of results. PipeOnline offers customization for individual projects (MyPipeOnline), automated updating and alert service. PipeOnline is available at http://stress-genomics.org.

MeSH Terms
Automation/methods Computational Biology/methods Consensus Sequence/genetics Conserved Sequence/genetics Databases, Genetic Databases, Protein Expressed Sequence Tags Genomics/methods Internet Open Reading Frames Sequence Alignment Sequence Homology, Amino Acid Software
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Ayoubi Patricia
Department of Microbiology and Molecular Genetics and. School of Mechanical and Aerospace Engineering, Oklahoma State University, Stillwater, OK 74078, USA.
Jin Xiaojing
Leite Saul
Liu Xianghui
Martajaja Jeson
Abduraham Abdurashid
Wan Qiaolan
Yan Wei
Misawa Eduardo
Prade Rolf A
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkf585
Published
2002-11-01
Pages
4761-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC135791
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkf585 PMC Full Text View journal details
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