ESTprep: preprocessing cDNA sequence reads.
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
Scheetz
Todd E
TE
Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, IA 52242, USA. tscheetz@eng.uiowa.edu
Trivedi
Nishank
N
Roberts
Chad A
CA
Kucaba
Tamara
T
Berger
Brian
B
Robinson
Natalie L
NL
Birkett
Clayton L
CL
Gavin
Allen J
AJ
O'Leary
Brian
B
Braun
Terry A
TA
Bonaldo
Maria F
MF
Robinson
John P
JP
Sheffield
Val C
VC
Soares
Marcelo B
MB
Casavant
Thomas L
TL
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
D018076:DNA, Complementary