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FusoBase: an online Fusobacterium comparative genomic analysis platform

Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, p...

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Autores principales: Ang, Mia Yang, Heydari, Hamed, Jakubovics, Nick S., Mahmud, Mahafizul Imran, Dutta, Avirup, Wee, Wei Yee, Wong, Guat Jah, Mutha, Naresh V.R., Tan, Shi Yang, Choo, Siew Woh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141642/
https://www.ncbi.nlm.nih.gov/pubmed/25149689
http://dx.doi.org/10.1093/database/bau082
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author Ang, Mia Yang
Heydari, Hamed
Jakubovics, Nick S.
Mahmud, Mahafizul Imran
Dutta, Avirup
Wee, Wei Yee
Wong, Guat Jah
Mutha, Naresh V.R.
Tan, Shi Yang
Choo, Siew Woh
author_facet Ang, Mia Yang
Heydari, Hamed
Jakubovics, Nick S.
Mahmud, Mahafizul Imran
Dutta, Avirup
Wee, Wei Yee
Wong, Guat Jah
Mutha, Naresh V.R.
Tan, Shi Yang
Choo, Siew Woh
author_sort Ang, Mia Yang
collection PubMed
description Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram. Database URL: http://fusobacterium.um.edu.my.
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spelling pubmed-41416422014-08-28 FusoBase: an online Fusobacterium comparative genomic analysis platform Ang, Mia Yang Heydari, Hamed Jakubovics, Nick S. Mahmud, Mahafizul Imran Dutta, Avirup Wee, Wei Yee Wong, Guat Jah Mutha, Naresh V.R. Tan, Shi Yang Choo, Siew Woh Database (Oxford) Original Article Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram. Database URL: http://fusobacterium.um.edu.my. Oxford University Press 2014-08-22 /pmc/articles/PMC4141642/ /pubmed/25149689 http://dx.doi.org/10.1093/database/bau082 Text en © The Author(s) 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Ang, Mia Yang
Heydari, Hamed
Jakubovics, Nick S.
Mahmud, Mahafizul Imran
Dutta, Avirup
Wee, Wei Yee
Wong, Guat Jah
Mutha, Naresh V.R.
Tan, Shi Yang
Choo, Siew Woh
FusoBase: an online Fusobacterium comparative genomic analysis platform
title FusoBase: an online Fusobacterium comparative genomic analysis platform
title_full FusoBase: an online Fusobacterium comparative genomic analysis platform
title_fullStr FusoBase: an online Fusobacterium comparative genomic analysis platform
title_full_unstemmed FusoBase: an online Fusobacterium comparative genomic analysis platform
title_short FusoBase: an online Fusobacterium comparative genomic analysis platform
title_sort fusobase: an online fusobacterium comparative genomic analysis platform
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141642/
https://www.ncbi.nlm.nih.gov/pubmed/25149689
http://dx.doi.org/10.1093/database/bau082
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