title: ESTprep: preprocessing cDNA sequence reads.
abstract: BACKGROUND
  High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases.
  
  
  RESULTS
  This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank.
  
  
  BACKGROUND
  The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html
authors.affiliation: Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IA 52242, USA. tscheetz@eng.uiowa.edu
authors.forename: Todd E
authors.initials: TE
authors.lastname: Scheetz
authors.forename: Nishank
authors.initials: N
authors.lastname: Trivedi
authors.forename: Chad A
authors.initials: CA
authors.lastname: Roberts
authors.forename: Tamara
authors.initials: T
authors.lastname: Kucaba
authors.forename: Brian
authors.initials: B
authors.lastname: Berger
authors.forename: Natalie L
authors.initials: NL
authors.lastname: Robinson
authors.forename: Clayton L
authors.initials: CL
authors.lastname: Birkett
authors.forename: Allen J
authors.initials: AJ
authors.lastname: Gavin
authors.forename: Brian
authors.initials: B
authors.lastname: O'Leary
authors.forename: Terry A
authors.initials: TA
authors.lastname: Braun
authors.forename: Maria F
authors.initials: MF
authors.lastname: Bonaldo
authors.forename: John P
authors.initials: JP
authors.lastname: Robinson
authors.forename: Val C
authors.initials: VC
authors.lastname: Sheffield
authors.forename: Marcelo B
authors.initials: MB
authors.lastname: Soares
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Casavant
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D018076:DNA, Complementary / Q000737:chemistry* / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D008969:Molecular Sequence Data; D011786:Quality Control; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D018076:DNA, Complementary