BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

Manal Kalkatawi,Intikhab Alam,Vladimir B Bajic

doi:10.1186/s12864-015-1826-4

Manal Kalkatawi, Intikhab Alam + Show 1 more

Open Access

https://doi.org/10.1186/s12864-015-1826-4

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Abstract

BackgroundGenome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs).ResultsThe presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced.ConclusionsWe developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1826-4) contains supplementary material, which is available to authorized users.

Highlights

Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism
Beacon: method and implementation In order to have automated, rapid, simple and informative genome annotation comparison we developed a tool, Bacterial GEnome Annotation ComparisON (BEACON), which can analyze and compare annotations generated by multiple annotation methods (AMs) and extend the annotation generated by an individual AM
As the first example to illustrate capabilities of BEACON, we used H. utahensis genome to compare the annotations by Annotation of Microbial Genomes (AAMG) and Rapid Annotations using Subsystems Technology (RAST) to the annotation from NCBI

Summary

Introduction

Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation Many methods for this purpose have been developed for eukaryotes and prokaryotes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). One of the potential uses of BEACON can be to update annotations for large number of microbial genomes that are deposited long time ago and are not updated since [6]. In these cases, multiple AMs can be deployed by BEACON

Results

Discussion

Conclusion