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CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulenc...

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Main Authors: Heydari, H., Siow, C.C., Tan, M.F., Jakubovics, N.S., Wee, W.Y., Mutha, N.V.R., Wong, G.J., Ang, M.Y., Yazdi, A.H., Choo, S.W.
Format: Article
Language:English
Published: Public Library of Science 2014
Subjects:
RK Dentistry
Online Access:http://eprints.um.edu.my/9865/1/Corynbase.pdf
http://eprints.um.edu.my/9865/
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spelling my.um.eprints.98652017-07-05T01:32:18Z http://eprints.um.edu.my/9865/ CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips Heydari, H. Siow, C.C. Tan, M.F. Jakubovics, N.S. Wee, W.Y. Mutha, N.V.R. Wong, G.J. Ang, M.Y. Yazdi, A.H. Choo, S.W. RK Dentistry Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/. Public Library of Science 2014 Article PeerReviewed application/pdf en http://eprints.um.edu.my/9865/1/Corynbase.pdf Heydari, H. and Siow, C.C. and Tan, M.F. and Jakubovics, N.S. and Wee, W.Y. and Mutha, N.V.R. and Wong, G.J. and Ang, M.Y. and Yazdi, A.H. and Choo, S.W. (2014) CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips. PLoS ONE, 9 (1). ISSN 1932-6203 10.1371/journal.pone.0086318
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Research Repository
url_provider http://eprints.um.edu.my/
language English
topic RK Dentistry
spellingShingle RK Dentistry
Heydari, H.
Siow, C.C.
Tan, M.F.
Jakubovics, N.S.
Wee, W.Y.
Mutha, N.V.R.
Wong, G.J.
Ang, M.Y.
Yazdi, A.H.
Choo, S.W.
CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips
description Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.
format Article
author Heydari, H.
Siow, C.C.
Tan, M.F.
Jakubovics, N.S.
Wee, W.Y.
Mutha, N.V.R.
Wong, G.J.
Ang, M.Y.
Yazdi, A.H.
Choo, S.W.
author_facet Heydari, H.
Siow, C.C.
Tan, M.F.
Jakubovics, N.S.
Wee, W.Y.
Mutha, N.V.R.
Wong, G.J.
Ang, M.Y.
Yazdi, A.H.
Choo, S.W.
author_sort Heydari, H.
title CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips
title_short CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips
title_full CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips
title_fullStr CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips
title_full_unstemmed CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips
title_sort corynebase: corynebacterium genomic resources and analysis tools at your fingertips
publisher Public Library of Science
publishDate 2014
url http://eprints.um.edu.my/9865/1/Corynbase.pdf
http://eprints.um.edu.my/9865/
_version_ 1643688672540753920
score 13.211869

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