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Publication for MetaRef
Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies
[…] 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
[…] 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
[…] 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
[…] 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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