Cover Image

StaphyloBase: a specialized genomic resource for the staphylococcal research community

With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by st...

Full description

Saved in:
Bibliographic Details
Main Authors: Heydari, H., Mutha, N.V.R., Mahmud, M.I., Siow, C.C., Wee, W.Y., Wong, G.J., Yazdi, A.H., Ang, M.Y., Choo, S.W.
Format: Article
Language:English
Published: 2014
Subjects:
RK Dentistry
Online Access:http://eprints.um.edu.my/9894/1/bau010.full.pdf
http://eprints.um.edu.my/9894/
Tags: Add Tag
No Tags, Be the first to tag this record!
id my.um.eprints.9894
record_format eprints
spelling my.um.eprints.98942014-10-29T00:33:53Z http://eprints.um.edu.my/9894/ StaphyloBase: a specialized genomic resource for the staphylococcal research community Heydari, H. Mutha, N.V.R. Mahmud, M.I. Siow, C.C. Wee, W.Y. Wong, G.J. Yazdi, A.H. Ang, M.Y. Choo, S.W. RK Dentistry With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. 2014 Article PeerReviewed application/pdf en http://eprints.um.edu.my/9894/1/bau010.full.pdf Heydari, H. and Mutha, N.V.R. and Mahmud, M.I. and Siow, C.C. and Wee, W.Y. and Wong, G.J. and Yazdi, A.H. and Ang, M.Y. and Choo, S.W. (2014) StaphyloBase: a specialized genomic resource for the staphylococcal research community. Database-the Journal of Biological Databases and Curation. ISSN 1758-0463
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.
Mutha, N.V.R.
Mahmud, M.I.
Siow, C.C.
Wee, W.Y.
Wong, G.J.
Yazdi, A.H.
Ang, M.Y.
Choo, S.W.
StaphyloBase: a specialized genomic resource for the staphylococcal research community
description With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses.
format Article
author Heydari, H.
Mutha, N.V.R.
Mahmud, M.I.
Siow, C.C.
Wee, W.Y.
Wong, G.J.
Yazdi, A.H.
Ang, M.Y.
Choo, S.W.
author_facet Heydari, H.
Mutha, N.V.R.
Mahmud, M.I.
Siow, C.C.
Wee, W.Y.
Wong, G.J.
Yazdi, A.H.
Ang, M.Y.
Choo, S.W.
author_sort Heydari, H.
title StaphyloBase: a specialized genomic resource for the staphylococcal research community
title_short StaphyloBase: a specialized genomic resource for the staphylococcal research community
title_full StaphyloBase: a specialized genomic resource for the staphylococcal research community
title_fullStr StaphyloBase: a specialized genomic resource for the staphylococcal research community
title_full_unstemmed StaphyloBase: a specialized genomic resource for the staphylococcal research community
title_sort staphylobase: a specialized genomic resource for the staphylococcal research community
publishDate 2014
url http://eprints.um.edu.my/9894/1/bau010.full.pdf
http://eprints.um.edu.my/9894/
_version_ 1643688678406488064
score 13.211869

Similar Items