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Bioinformatics Vol. 19 no. 13 2003
Pages 1712-1713
© 2003 Oxford University Press

Applications Note

GFPE: gene-finding program evaluation

Jian Wang and Eileen Kraemer *

Computer Science Department, The University of Georgia, Athens, GA 30602, USA

Received on September 26, 2002 ; revised on January 24, 2003 ; accepted on March 7, 2003

Summary: Gene-finding program evaluation (GFPE) is a set of Java classes for evaluating gene-finding programs. A command-line interface is also provided. Inputs to the program include the sequence data (in FASTA format), annotations of 'actual' sequence features, and annotations of 'predicted' sequence features. Annotation files are in the General Feature Format promoted by the Sanger center. GFPE calculates a number of metrics of accuracy of predictions at three levels: the coding level, the exon level, and the protein level.

Availability: The program is freely available at: ftp://anonymous@iubio.bio.indiana.edu/molbio/genefind/

Contact: eileen{at}cs.uga.edu

* To whom correspondence should be addressed.


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