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Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(10) © Oxford University Press 2004; all rights reserved.

Development of joint application strategies for two microbial gene finders

Alice C. McHardy 1, Alexander Goesmann 1, Alfred Pühler 2 and Folker Meyer 1,*

1 Center for Biotechnology (CeBiTec) and 2 Lehrstuhl für Genetik, Department of Biology, Bielefeld University, 33594 Bielefeld, Germany

Received on August 18, 2003; revised on December 19, 2003; accepted on January 15, 2004
Advance Access Publication February 26, 2004

Motivation: As a starting point in annotation of bacterial genomes, gene finding programs are used for the prediction of functional elements in the DNA sequence. Due to the faster pace and increasing number of genome projects currently underway, it is becoming especially important to have performant methods for this task.

Results: This study describes the development of joint application strategies that combine the strengths of two microbial gene finders to improve the overall gene finding performance. Critica is very specific in the detection of similarity-supported genes as it uses a comparative sequence analysis-based approach. Glimmer employs a very sophisticated model of genomic sequence properties and is sensitive also in the detection of organism-specific genes. Based on a data set of 113 microbial genome sequences, we optimized a combined application approach using different parameters with relevance to the gene finding problem. This results in a significant improvement in specificity while there is similarity in sensitivity to Glimmer. The improvement is especially pronounced for GC rich genomes. The method is currently being applied for the annotation of several microbial genomes.

Availability: The methods described have been implemented within the gene prediction component of the GenDB genome annotation system.

Contact: fm{at}CeBiTec.Uni-Bielefeld.DE

* To whom correspondence should be addressed.


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