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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science
2014
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| Online Access: | http://eprints.um.edu.my/9865/1/Corynbase.pdf |
| _version_ | 1825719775595069440 |
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| 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. |
| collection | UM |
| 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/. |
| first_indexed | 2024-03-06T05:24:55Z |
| format | Article |
| id | um.eprints-9865 |
| institution | Universiti Malaya |
| language | English |
| last_indexed | 2024-03-06T05:24:55Z |
| publishDate | 2014 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | 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, DOI https://doi.org/10.1371/journal.pone.0086318 <https://doi.org/10.1371/journal.pone.0086318>. 10.1371/journal.pone.0086318 |
| 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 |
| title | 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_short | CoryneBase: corynebacterium genomic resources and analysis tools at your fingertips |
| title_sort | corynebase corynebacterium genomic resources and analysis tools at your fingertips |
| topic | RK Dentistry |
| url | http://eprints.um.edu.my/9865/1/Corynbase.pdf |
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