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MetaBioME specifications

Information


Unique identifier OMICS_11135
Name MetaBioME
Alternative name Metagenomic BioMining Engine
Restrictions to use None
Data access Browse
Maintained Yes

Maintainer


  • person_outline Todd D. Taylor

Publication for Metagenomic BioMining Engine

MetaBioME citations

 (5)
library_books

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

2015
Front Genet
PMCID: 4681832
PMID: 26734060
DOI: 10.3389/fgene.2015.00348

[…] ical information as well. However, a limitation of this approach is the size and phylogenetic coverage of the database (Carr and Borenstein, ).Searches in customized databases such as CAZY, dbCAN, or MetaBioMe are alternative to avoid time consuming and the use of excessive computational resources in the annotation of genes related to a metabolic pathway (Teeling and Glöckner, ; Yang et al., ). In […]

library_books

Databases for Microbiologists

2015
J Bacteriol
PMCID: 4505447
PMID: 26013493
DOI: 10.1128/JB.00330-15

[…] conservation, and genome context comparisons. To promote inference of metagenomic functional networks, the MetaProx database () contains information on candidate operons in metagenomic data sets. The MetaBioME database () positions itself as a comprehensive metagenomic biomining engine by providing the opportunity to find novel homologs of known commercially useful enzymes in metagenomic data sets […]

library_books

Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective

2012
Brief Bioinform
PMCID: 3504927
PMID: 22966151
DOI: 10.1093/bib/bbs039

[…] ble for special functions, for example the CAZY [, ] and dbCAN (http://csbl.bmb.uga.edu/dbCAN/) databases for carbohydrate-active enzymes, the TSdb [] and TCDB [, ] databases for transporters and the MetaBioMe [] database for enzymes with biotechnological prospects. The resulting annotations are then used as a basis for functional data mining including metabolic reconstruction. Dedicated metagenom […]

library_books

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

2012
PLoS One
PMCID: 3253082
PMID: 22238585
DOI: 10.1371/journal.pone.0028967

[…] rome P450, lipases, proteases, phytases and dioxygenases, identified cDNAs were further filtered by BLASTX (default parameter, E-value≤10−6) against a curated database of commercially useful enzymes (MetaBioME, http://metasystems.riken.jp/metabiome/index.php, ) to retain only sequences similar to enzymes, which have known applications in industries. To identify full-length sequences, annotated cDN […]

library_books

Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

2010
Mar Drugs
PMCID: 2857354
PMID: 20411118
DOI: 10.3390/md8030608

[…] al capability of microbial communities based on their metagenome sequence by allowing comparative analysis of genome and metagenome sequences available on the JGI-Integrated Microbial Genomes system; MetaBioME [], which is a resource specifically aimed at novel enzyme discovery from metagenomic data; and Orphelia, which is a tool for discovering ORFs in short metagenomic sequences of unknown phylo […]

Citations

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MetaBioME institution(s)
MetaSystems Research Team, Computational Systems Biology Research Group, Advanced Computational Sciences Department, Advanced Science Institute, RIKEN, Yokohama, Kanagawa, Japan

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