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Nucleic Acids Research 2005 33(Web Server Issue):W677-W680; doi:10.1093/nar/gki394
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

OrfPredictor: predicting protein-coding regions in EST-derived sequences

Xiang Jia Min1,*, Gregory Butler1,2, Reginald Storms1,3 and Adrian Tsang1,3

1Centre for Structural and Functional Genomics, Concordia University Montreal, Quebec, Canada H4B 1R6 2Department of Computer Science, Concordia University Montreal, Quebec, Canada H4B 1R6 3Department of Biology, Concordia University Montreal, Quebec, Canada H4B 1R6

*To whom correspondence should be addressed. Tel: +1 514 848 2424, ext. 5791; Fax: +1 514 848 4504; Email: jack{at}gene.concordia.ca

Received February 12, 2005. Revised March 11, 2005. Accepted March 11, 2005.

OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at https://fungalgenome.concordia.ca/tools/OrfPredictor.html.


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