PanGFR-HM Edit

Citations: 0

z-index: 0

Basic information
Short name PanGFR-HM
Full name
Description a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project.
URL http://www.bioinfo.iicb.res.in/pangfr-hm
Year founded
Last update & version
Availability Free to academic users only
Contact information
University/Institution hosted CSIR - Indian Institute of Chemical Biology
Address
City Kolkata
Province/State
Country/Region India
Contact name (PI/Team) Sandip Paul
Contact email (PI/Helpdesk) sandippaul@iicb.res.in
Data information
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Data type
Database category
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Keyword
Publications
  • PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features. [PMID: 30349509]
    Narendrakumar M Chaudhari, Anupam Gautam, Vinod Kumar Gupta, Gagneet Kaur, Chitra Dutta, Sandip Paul

    The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) - a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics.

    Front Microbiol 2018:9()

    0 Citations (from Europe PMC, 2019-04-13)

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    • Gene genome and annotation: No. 0
The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of PanGFR-HM.

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Record metadata

  • Created on: 2019-01-04
    • ***ina@***c.cn [2019-01-23]
    • ***d@***c.cn [2019-01-12]
    • ***d@***c.cn [2019-01-12]
    • ***d@***c.cn [2019-01-04]

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