Database Commons a catalog of biological databases

Database Commons - MetaRef

MetaRef

Citations: 9

z-index 1.62

Short name MetaRef
Full name A pan-genomic database for microbial genomics
Description A pan-genomic database for comparative and community microbial genomics
URL http://metaref.org/
Year founded 2013
Last update & version 2013-11-06    v1.0
Availability Free to all users
University/Institution hosted University of Trento
Address via Sommarive 14, 38123 Povo (Trento)
City
Province/State
Country/Region Italy
Contact name Nicola Segata
Contact email nicola.segata@unitn.it
Data type(s)
Major organism(s)
Keyword(s)
  • gene family
  • microbial genomics
Publication(s)
  • MetaRef: a pan-genomic database for comparative and community microbial genomics. [PMID: 24203705]

    Katherine Huang, Arthur Brady, Anup Mahurkar, Owen White, Dirk Gevers, Curtis Huttenhower, Nicola Segata
    Nucleic acids research 2014:42(Database issue)
    9 Citations (Google Scholar as of 2016-01-28)

    Abstract: Microbial genome sequencing is one of the longest-standing areas of biological database development, but high-throughput, low-cost technologies have increased its throughput to an unprecedented number of new genomes per year. Several thousand microbial genomes are now available, necessitating new approaches to organizing information on gene function, phylogeny and microbial taxonomy to facilitate downstream biological interpretation. MetaRef, available at http://metaref.org, is a novel online resource systematically cataloguing a comprehensive pan-genome of all microbial clades with sequenced isolates. It organizes currently available draft and finished bacterial and archaeal genomes into quality-controlled clades, reports all core and pan gene families at multiple levels in the resulting taxonomy, and it annotates families' conservation, phylogeny and consensus functional information. MetaRef also provides a comprehensive non-redundant reference gene catalogue for metagenomic studies, including the abundance and prevalence of all gene families in the >700 shotgun metagenomic samples of the Human Microbiome Project. This constitutes a systematic mapping of clade-specific microbial functions within the healthy human microbiome across multiple body sites and can be used as reference for identifying potential functional biomarkers in disease-associate microbiomes. MetaRef provides all information both as an online browsable resource and as downloadable sequences and tabular data files that can be used for subsequent offline studies.

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200 OK2016-02-01
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200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
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200 OK2016-01-20
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200 OK2016-01-17
200 OK2016-01-15
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Tags

DNA
Archaea Bacteria
gene family microbial genomics

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Zhang Zhang [2016-05-08]
    • Lin Liu [2016-04-16]
    • Lin Liu [2016-03-26]
    • Li Yang [2015-06-26]
Stats