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 |
| Published: |
Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3895029?pdf=render |
| _version_ | 1828259786735484928 |
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| author | Hamed Heydari Cheuk Chuen Siow Mui Fern Tan Nick S Jakubovics Wei Yee Wee Naresh V R Mutha Guat Jah Wong Mia Yang Ang Amir Hessam Yazdi Siew Woh Choo |
| author_facet | Hamed Heydari Cheuk Chuen Siow Mui Fern Tan Nick S Jakubovics Wei Yee Wee Naresh V R Mutha Guat Jah Wong Mia Yang Ang Amir Hessam Yazdi Siew Woh Choo |
| author_sort | Hamed Heydari |
| collection | DOAJ |
| 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 | 2024-04-13T03:13:54Z |
| format | Article |
| id | doaj.art-3fd2caad6a1f4fbeb52c3c11c67b72a8 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T03:13:54Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3fd2caad6a1f4fbeb52c3c11c67b72a82022-12-22T03:04:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0191e8631810.1371/journal.pone.0086318CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips.Hamed HeydariCheuk Chuen SiowMui Fern TanNick S JakubovicsWei Yee WeeNaresh V R MuthaGuat Jah WongMia Yang AngAmir Hessam YazdiSiew Woh ChooCorynebacteria 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/.http://europepmc.org/articles/PMC3895029?pdf=render |
| spellingShingle | Hamed Heydari Cheuk Chuen Siow Mui Fern Tan Nick S Jakubovics Wei Yee Wee Naresh V R Mutha Guat Jah Wong Mia Yang Ang Amir Hessam Yazdi Siew Woh Choo CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips. PLoS ONE |
| 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 |
| url | http://europepmc.org/articles/PMC3895029?pdf=render |
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