Introduction

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

Publications

  1. ESTprep: preprocessing cDNA sequence reads.
    Cite this
    Scheetz TE, Trivedi N, Roberts CA, Kucaba T, Berger B, Robinson NL, Birkett CL, Gavin AJ, O'Leary B, Braun TA, Bonaldo MF, Robinson JP, Sheffield VC, Soares MB, Casavant TL, 2003-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Todd E Scheetz
    Developer

  2. Nishank Trivedi
    Developer

  3. Chad A Roberts
    Developer

  4. Tamara Kucaba
    Developer

  5. Brian Berger
    Developer

  6. Natalie L Robinson
    Developer

  7. Clayton L Birkett
    Developer

  8. Allen J Gavin
    Developer

  9. Brian O'Leary
    Developer

  10. Terry A Braun
    Developer

  11. Maria F Bonaldo
    Developer

  12. John P Robinson
    Developer

  13. Val C Sheffield
    Developer

  14. Marcelo B Soares
    Developer

  15. Thomas L Casavant
    Investigator

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Summary
AccessionBT002440
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByThomas L Casavant