BEACON: automated tool for Bacterial GEnome Annotation ComparisON

Handle URI:
http://hdl.handle.net/10754/575255
Title:
BEACON: automated tool for Bacterial GEnome Annotation ComparisON
Authors:
Kalkatawi, Manal M. ( 0000-0002-9820-4129 ) ; Alam, Intikhab; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Background 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. 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). Results The 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. Conclusions We 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/
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
BEACON: automated tool for Bacterial GEnome Annotation ComparisON 2015, 16 (1) BMC Genomics
Publisher:
Springer Science + Business Media
Journal:
BMC Genomics
Issue Date:
18-Aug-2015
DOI:
10.1186/s12864-015-1826-4
Type:
Article
ISSN:
1471-2164
Is Supplemented By:
Kalkatawi, M., Intikhab Alam, & Bajic, V. (2015). BEACON: automated tool for Bacterial GEnome Annotation ComparisON. Figshare. https://doi.org/10.6084/m9.figshare.c.3616301; DOI:10.6084/m9.figshare.c.3616301; HANDLE:http://hdl.handle.net/10754/624132
Additional Links:
http://www.biomedcentral.com/1471-2164/16/616
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorKalkatawi, Manal M.en
dc.contributor.authorAlam, Intikhaben
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2015-08-19T12:25:40Zen
dc.date.available2015-08-19T12:25:40Zen
dc.date.issued2015-08-18en
dc.identifier.citationBEACON: automated tool for Bacterial GEnome Annotation ComparisON 2015, 16 (1) BMC Genomicsen
dc.identifier.issn1471-2164en
dc.identifier.doi10.1186/s12864-015-1826-4en
dc.identifier.urihttp://hdl.handle.net/10754/575255en
dc.description.abstractBackground 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. 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). Results The 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. Conclusions We 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/en
dc.language.isoenen
dc.publisherSpringer Science + Business Mediaen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/16/616en
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en
dc.subjectGenome annotation comparisonen
dc.subjectGene function annotationen
dc.subjectFunctional annotation of bacterial genomesen
dc.subjectAnnotation methodsen
dc.subjectBioinformaticsen
dc.titleBEACON: automated tool for Bacterial GEnome Annotation ComparisONen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBMC Genomicsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorKalkatawi, Manal M.en
kaust.authorAlam, Intikhaben
kaust.authorBajic, Vladimir B.en
dc.relation.isSupplementedByKalkatawi, M., Intikhab Alam, & Bajic, V. (2015). BEACON: automated tool for Bacterial GEnome Annotation ComparisON. Figshare. https://doi.org/10.6084/m9.figshare.c.3616301en
dc.relation.isSupplementedByDOI:10.6084/m9.figshare.c.3616301en
dc.relation.isSupplementedByHANDLE:http://hdl.handle.net/10754/624132en
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