ESTprep: preprocessing cDNA sequence reads

Todd E Scheetz; Nishank Trivedi; Chad A Roberts; Tamara Kucaba; Brian Berger; Natalie L Robinson; Clayton L Birkett; Allen J Gavin; Brian O'Leary; Terry A Braun; Maria F Bonaldo; John P Robinson; Val C Sheffield; Marcelo B Soares; Thomas L Casavant

doi:10.1093/bioinformatics/btg159

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ESTprep: preprocessing cDNA sequence reads

Journal article

Open access

Peer reviewed

ESTprep: preprocessing cDNA sequence reads

Todd E Scheetz, Nishank Trivedi, Chad A Roberts, Tamara Kucaba, Brian Berger, Natalie L Robinson, Clayton L Birkett, Allen J Gavin, Brian O'Leary, Terry A Braun, …

Bioinformatics (Oxford, England), Vol.19(11), pp.1318-1324

07/22/2003

DOI: 10.1093/bioinformatics/btg159

PMID: 12874042

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Abstract

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. 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. The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html

Sequence Alignment - methods

Algorithms

Base Sequence

DNA, Complementary - genetics

Molecular Sequence Data

Gene Expression Profiling - methods

Software

DNA, Complementary - chemistry

Sequence Analysis, DNA - methods

Expressed Sequence Tags

Quality Control

Details

Title: Subtitle: ESTprep: preprocessing cDNA sequence reads
Creators: Todd E Scheetz - Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IA 52242, USA. tscheetz@eng.uiowa.edu
Nishank Trivedi
Chad A Roberts
Tamara Kucaba
Brian Berger
Natalie L Robinson
Clayton L Birkett
Allen J Gavin
Brian O'Leary
Terry A Braun
Maria F Bonaldo
John P Robinson
Val C Sheffield
Marcelo B Soares
Thomas L Casavant
Resource Type: Journal article
Publication Details: Bioinformatics (Oxford, England), Vol.19(11), pp.1318-1324
Publisher: England
DOI: 10.1093/bioinformatics/btg159
PMID: 12874042
ISSN: 1367-4803
eISSN: 1367-4811
Language: English
Date published: 07/22/2003
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Stead Family Department of Pediatrics; Medical Genetics and Genomics; Biology; Ophthalmology and Visual Sciences
Record Identifier: 9983979978402771

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