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MetaRef specifications


Unique identifier OMICS_11136
Name MetaRef
Restrictions to use None
Data access File download, Browse
Version 1.0
Maintained No


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Publication for MetaRef

MetaRef citations


Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

Int J Mol Sci
PMCID: 5855605
PMID: 29382070
DOI: 10.3390/ijms19020383

[…] eneMark [], and Glimmer-MG [], have been developed and optimized for this aim. Once the genes have been identified, specific databases can be used for functional predictions, such as IMG database [], MetaRef [], dbCAN [], and HUMAnN [] ().Since the data obtained with this shotgun approach are more complete than those from simple 16S rRNAs or ITS (Internal Transcribed Spacer) analyses, it is concei […]


Probing the diversity of healthy oral microbiome with bioinformatics approaches

PMCID: 5346311
PMID: 27697111
DOI: 10.5483/BMBRep.2016.49.12.164

[…] After gene prediction, the identified genes are functionally annotated by comparing the known genes in the functional annotation databases such as PFAM (), IMG/M (), COG () and MetaRef (). Further analysis of the relationship between the microbiome and the host phenotype is performed using metabolic pathway information database, i.e. KEGG (), eggNOG () and MinPath (). In the […]


Databases for Microbiologists

J Bacteriol
PMCID: 4505447
PMID: 26013493
DOI: 10.1128/JB.00330-15

[…] n automated pipeline. Similar capabilities are provided by IMG in its dedicated IMG/M resource (), which also enables expert review of metagenome annotations (IMG/M ER). The metaMicrobesOnline () and MetaRef () databases offer comparative analysis for microbial genomes and metagenomes with emphasis on gene trees, gene family conservation, and genome context comparisons. To promote inference of met […]


The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

Nucleic Acids Res
PMCID: 3965027
PMID: 24316579
DOI: 10.1093/nar/gkt1282

[…] base Project (RDP), the Silva/LTP project, BacDive at the DSMZ-German Collection of Microorganisms and Cell Cultures and the List of Prokaryotic Names with Standing in Nomenclature (LPSN) (). The new MetaRef database collects from reference microbial genomes clade-specific genes that could be useful for taxonomic assignments of metagenomic reads ().One of the major highlights of this issue is the […]


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MetaRef institution(s)
Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Biostatistics Department, Harvard School of Public Health, Boston, MA, USA; Centre for Integrative Biology, University of Trento, Povo (Trento), Italy
MetaRef funding source(s)
National Institutes of Health [R01HG005969]; National Science Foundation [DBI-1053486]; Danone Research [PLF-5972-GD to Wendy Garrett]; This project has been funded in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract [No.: HHSN272200900018C], and with funds from the National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services [U54HG004969 to the Broad Institute]. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement [PCIG13-GA-2013-618833].

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