VibrioBase: A Model for Next-Generation Genome and Annotation Database Development
To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence...
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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1155/2014/569324 |
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| author | Siew Woh Choo Hamed Heydari Tze King Tan Cheuk Chuen Siow Ching Yew Beh Wei Yee Wee Naresh V. R. Mutha Guat Jah Wong Mia Yang Ang Amir Hessam Yazdi |
| author_facet | Siew Woh Choo Hamed Heydari Tze King Tan Cheuk Chuen Siow Ching Yew Beh Wei Yee Wee Naresh V. R. Mutha Guat Jah Wong Mia Yang Ang Amir Hessam Yazdi |
| author_sort | Siew Woh Choo |
| collection | DOAJ |
| description | To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development. |
| format | Article |
| id | doaj-art-bc20d639e1b446009736a9fe9c740d7f |
| institution | Kabale University |
| issn | 2356-6140 1537-744X |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-bc20d639e1b446009736a9fe9c740d7f2025-02-03T05:50:58ZengWileyThe Scientific World Journal2356-61401537-744X2014-01-01201410.1155/2014/569324569324VibrioBase: A Model for Next-Generation Genome and Annotation Database DevelopmentSiew Woh Choo0Hamed Heydari1Tze King Tan2Cheuk Chuen Siow3Ching Yew Beh4Wei Yee Wee5Naresh V. R. Mutha6Guat Jah Wong7Mia Yang Ang8Amir Hessam Yazdi9Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaGenome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaGenome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaGenome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, MalaysiaTo facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development.http://dx.doi.org/10.1155/2014/569324 |
| spellingShingle | Siew Woh Choo Hamed Heydari Tze King Tan Cheuk Chuen Siow Ching Yew Beh Wei Yee Wee Naresh V. R. Mutha Guat Jah Wong Mia Yang Ang Amir Hessam Yazdi VibrioBase: A Model for Next-Generation Genome and Annotation Database Development The Scientific World Journal |
| title | VibrioBase: A Model for Next-Generation Genome and Annotation Database Development |
| title_full | VibrioBase: A Model for Next-Generation Genome and Annotation Database Development |
| title_fullStr | VibrioBase: A Model for Next-Generation Genome and Annotation Database Development |
| title_full_unstemmed | VibrioBase: A Model for Next-Generation Genome and Annotation Database Development |
| title_short | VibrioBase: A Model for Next-Generation Genome and Annotation Database Development |
| title_sort | vibriobase a model for next generation genome and annotation database development |
| url | http://dx.doi.org/10.1155/2014/569324 |
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