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S. P. Shah, G. P. McVicker, Alan K. Mackworth, S. Rogic, and B. F. F. Quellette. GeneComber: Combining Outputs of Gene Prediction Programs for Improved Results. Bioinformatics, 19(10):1296–1297, 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.
@Article{Bioinformatics03,
author = {S. P. Shah and G. P. McVicker and Alan K. Mackworth and S. Rogic and B. F. F. Quellette},
title = {GeneComber: Combining Outputs of Gene Prediction Programs for Improved Results},
year = {2003},
journal = {Bioinformatics},
volume = {19},
number = {10},
pages = {1296--1297},
abstract = {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. },
bib2html_pubtype ={Refereed Journal},
bib2html_rescat ={},
}
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