General Feature Format Research Articles

GFPE: gene-finding program evaluation

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.

GeneComber: combining outputs of gene prediction programs for improved results.

We recently demonstrated that combining the output from Genscan and HMMgene can provide increased accuracy of gene predictions. We have created a robust software system that runs algorithms previously described on DNA sequences and provides a public web interface to the system for use by the biological community worldwide. The GeneComber system performs ab initio gene prediction by first taking a user inputted DNA sequence and running Genscan and HMMgene. The outputs of Genscan and HMMgene are then integrated using the EUI, GI and EUI_frame algorithms. All results are then stored into a relational database management system (RDBMS) and can then be retrieved through a web interface. The web interface provides a unified view of the GeneComber predictions by graphically overlaying outputs from Genscan, HMMgene, EUI, GI and EUI_frame. Outputs can also be retrieved in general feature format (GFF) or FASTA format. The software is written in the Perl programming language and is both dependent on and interoperable with the Bioperl toolkit. It includes high-level application programming interfaces (APIs) to run Genscan, HMMgene and a database API to insert prediction results into an RDBMS. The APIs are assembled into the genecomber script which is executed by the web interface or can be run directly from the Unix command line. The web interface is written in PHP and is structured so as to be easily modified for viewing data from any database that stores gene structures. The GeneComber public web interface and supplementary information is located at http://bioinformatics.ubc.ca/genecomber The source code is released under the GNU General Public License and is available at ftp://ftp.bioinformatics.ubc.ca/pub/genecomber/software.