BEACON: automated tool for Bacterial GEnome Annotation ComparisON.
Manal Kalkatawi1, Intikhab Alam2, Vladimir B Bajic3
1Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia. manal.kalkatawi@kaust.edu.sa.
BMC Genomics
|August 19, 2015
Summary
We developed BEACON, an automated tool for comparing bacterial genome annotations. This system enhances functional gene assignments, reducing unannotated genes by up to 27%.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Genome annotation summarizes genomic characteristics, with growing interest in computational methods.
- Numerous structural and functional genome annotation methods exist for prokaryotes and eukaryotes.
- A gap exists in automated systems for detailed comparison of functional genome annotations from different methods.
Purpose of the Study:
- To develop a system for automated, detailed comparison of functional genome annotations from different annotation methods (AMs).
- To create a tool that aids both AM developers and annotation analyzers.
- To generate extended genome annotations by combining individual ones.
Main Methods:
- Development of the Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON).
- BEACON enables detailed comparison of gene function annotations from multiple AMs.
- BEACON generates extended annotations by combining outputs from individual AMs.
Main Results:
- BEACON facilitates comparison and combination of prokaryotic genome annotations.
- Analysis of four genomes showed extended annotations increased putative gene functions by up to 27%.
- The number of genes lacking any function assignment was reduced using BEACON's combined annotations.
Conclusions:
- BEACON is a fast, automated tool for systematic comparison of genome annotations.
- Extended annotations generated by BEACON assign putative functions to previously unannotated genes.
- BEACON is freely available under GNU GPL v3.0.
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