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A novel hybrid gene prediction method employing protein multiple sequence alignments
Oliver Keller1, Martin Kollmar, Mario Stanke
1Institute of Computer Science, University of Göttingen, Goldschmidtstrasse 7, Greifswald, Germany. keller@cs.uni-goettingen.de
Bioinformatics (Oxford, England)
|January 11, 2011
Summary
Automated gene prediction software AUGUSTUS now uses protein family profiles for enhanced accuracy. This method significantly increases the rate of correctly predicted genes in eukaryotic genome assemblies.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Advancements in DNA sequencing necessitate improved automated gene prediction methods for eukaryotic genomes.
- Protein family classification can provide complementary data for gene prediction.
Purpose of the Study:
- To enhance the accuracy of the AUGUSTUS gene prediction software.
- To integrate protein family information into gene prediction.
Main Methods:
- Extended the AUGUSTUS gene prediction software.
- Implemented a method using block profiles from multiple sequence alignments as protein signatures.
- Utilized profiles for human dynein heavy chain (DHC) proteins and other families.
Main Results:
- Achieved a dramatic increase in the rate of highly accurate gene predictions.
- Demonstrated improved performance compared to the ab initio version of AUGUSTUS.
Conclusions:
- The integration of protein family profiles significantly enhances gene prediction accuracy.
- This approach offers a valuable complementary strategy for eukaryotic genome annotation.
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