title: PipeOnline 2.0: automated EST processing and functional data sorting.
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.
authors.affiliation: Department of Microbiology and Molecular Genetics and. School of Mechanical and Aerospace Engineering, Oklahoma State University, Stillwater, OK 74078, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Ayoubi
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Jin
authors.forename: Saul
authors.initials: S
authors.lastname: Leite
authors.forename: Xianghui
authors.initials: X
authors.lastname: Liu
authors.forename: Jeson
authors.initials: J
authors.lastname: Martajaja
authors.forename: Abdurashid
authors.initials: A
authors.lastname: Abduraham
authors.forename: Qiaolan
authors.initials: Q
authors.lastname: Wan
authors.forename: Wei
authors.initials: W
authors.lastname: Yan
authors.forename: Eduardo
authors.initials: E
authors.lastname: Misawa
authors.forename: Rolf A
authors.initials: RA
authors.lastname: Prade
mesh_terms: D001331:Automation / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D030541:Databases, Genetic; D030562:Databases, Protein; D020224:Expressed Sequence Tags; D023281:Genomics / Q000379:methods; D020407:Internet; D016366:Open Reading Frames; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software