Bioinformatics Vol. 19 no. 10 2003
Pages 1296-1297
© 2003 Oxford University Press
Applications Note |
GeneComber: combining outputs of gene prediction programs for improved results
1 UBC Bioinformatics Centre,
University of British Columbia, 950 28th Ave W, Vancouver BC, V5Z4H4 Canada
2 Department of Computer Science,
University of Brtish Columbia, 201-2366 Main Mall, Vancouver BC, V6T1Z4 Canada
Received on November 20, 2002
; revised on January 15, 2003
; accepted on January 20, 2003
Summary: 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.
Availability: 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
Contact: francis{at}bioinformatics.ubc.ca
* To whom correspondence should be addressed.
Present address: EMBL - European Bioinformatics Institute,
Cambridge CB10 1SD, UK.
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