Please use this identifier to cite or link to this item: https://hdl.handle.net/20.500.12540/105
DC FieldValueLanguage
dc.contributor.authorChoo, Siew W.en_US
dc.contributor.authorAng, Mia Y.en_US
dc.contributor.authorFouladi, Haniehen_US
dc.contributor.authorTan, Shi Y.en_US
dc.contributor.authorSiow, Cheuk C.en_US
dc.contributor.authorMutha, Naresh VR.en_US
dc.contributor.authorHeydari, Hameden_US
dc.contributor.authorWee, Wei Y.en_US
dc.contributor.authorVadivelu, Jamunaen_US
dc.contributor.authorLoke, Mun F.en_US
dc.contributor.authorRehvathy, Vellayaen_US
dc.contributor.authorWong, Guat J.en_US
dc.date.accessioned2020-07-21T02:11:45Z-
dc.date.available2020-07-21T02:11:45Z-
dc.date.issued2014-
dc.identifier.citationChoo, S. W., Ang, M. Y., Fouladi, H., Tan, S. Y., Siow, C. C., Mutha, N. V., ... & Rehvathy, V. (2014). HelicoBase: A Helicobacter genomic resource and analysis platform. BMC Genomics, 15, 600.en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12540/105-
dc.description.abstractBackground: Helicobacter is a genus of Gram-negative bacteria, possessing a characteristic helical shape that has been associated with a wide spectrum of human diseases. Although much research has been done on Helicobacter and many genomes have been sequenced, currently there is no specialized Helicobacter genomic resource and analysis platform to facilitate analysis of these genomes. With the increasing number of Helicobacter genomes being sequenced, 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 diseases caused by Helicobacter pathogens.en_US
dc.description.abstractDescription: To facilitate the ongoing research on Helicobacter, a specialized central repository and analysis platform for the Helicobacter research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data, particularly comparative analysis. Here we present HelicoBase, a user-friendly Helicobacter resource platform with diverse functionality for the analysis of Helicobacter genomic data for the Helicobacter research communities. HelicoBase hosts a total of 13 species and 166 genome sequences of Helicobacter spp. Genome annotations such as gene/protein sequences, protein function and sub-cellular localisation are also included. Our web implementation supports diverse query types and seamless searching of annotations using an AJAX-based real-time searching system. JBrowse is also incorporated to allow rapid and seamless browsing of Helicobacter genomes and annotations. Advanced bioinformatics analysis tools consisting of standard BLAST for similarity search, VFDB BLAST for sequence similarity 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 are also included to facilitate the analysis of Helicobacter genomic data.en_US
dc.description.abstractConclusions: HelicoBase offers access to a range of genomic resources as well as tools for the analysis of Helicobacter genome data. HelicoBase can be accessed at http://helicobacter.um.edu.my.en_US
dc.format.extent12 pagesen_US
dc.format.mimetypeapplication/pdfen_US
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.relation.ispartofBMC Genomicsen_US
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/-
dc.subject.lcshHelicobacteren_US
dc.subject.lcshComparative Analysisen_US
dc.titleHelicoBase: A Helicobacter genomic resource and analysis platformen_US
dc.typeArticleen_US
dc.rights.licenseAttribution-NonCommercial 4.0 International (CC BY-NC 4.0)en_US
dc.identifier.doi10.1186/1471-2164-15-600-
dc.subject.keywordsHelicoBaseen_US
dc.subject.keywordsGenomic Resourcesen_US
dc.subject.keywordsPairwise Genome Comparison Toolen_US
dc.subject.keywordsPathogenomics Profiling Toolen_US
Appears in Collections:Scholarly Publications
Files in This Item:
File Description SizeFormat 
wku_schlrs_publcn_000078.pdf2.65 MBAdobe PDFThumbnail
View/Open
Show simple item record

Page view(s)

745
checked on Mar 29, 2024

Download(s)

176
checked on Mar 29, 2024

Google ScholarTM

Check

Altmetric


This item is licensed under a Creative Commons License Creative Commons