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ggKbase specifications

Information


Unique identifier OMICS_32500
Name ggKbase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Jillian Banfield

Publication for ggKbase

ggKbase citations

 (17)
library_books

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

2018
MBio
PMCID: 5893878
PMID: 29636439
DOI: 10.1128/mBio.00441-18

[…] BLAST () hits to the genomes assembled in the prior study.As part of the NIH2 and NIH3 studies, scaffolds were binned based on their GC content, DNA sequence coverage, and taxonomic affiliation using ggKbase tools (ggkbase.berkeley.edu). Genome bins from all three data sets were classified based on the consensus of taxonomic assignments for predicted protein sequences. Genome completeness and cont […]

library_books

Strain resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

2017
Nat Commun
PMCID: 5703836
PMID: 29180750
DOI: 10.1038/s41467-017-02018-w

[…] e saved as were reciprocal best hits with scores greater than 300. Ribosomal RNA sequences were identified using Infernal, and tRNAs with tRNAscan_SE. Binning of fecal samples was conducted using the ggKbase binning interface. Binning of room samples was conducted using DAS Tool v1.0 using bins from CONCOCT v0.4.1, ABAWACA v1.00 (https://github.com/CK7/abawaca), and MaxBin v2.2 as input. To derepl […]

library_books

Members of the Candidate Phyla Radiation are functionally differentiated by carbon and nitrogen cycling capabilities

2017
Microbiome
PMCID: 5581439
PMID: 28865481
DOI: 10.1186/s40168-017-0331-1

[…] [] was also used to visualize pathway completeness.The presence of different glycoside hydrolase (GH) families was determined in both the above bins and 2155 previously studied genomes obtained from ggkbase [, ] by using the dbCAN hidden Markov model (HMM) (hmmsearch --cpu 4 --tblout result.hres --noali -E 0.00001 -o result_hmm.txt dbCAN-fam-HMMs.hmm input.faa) [–]. Using the hmmsearch output, GH […]

library_books

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

2017
Sci Data
PMCID: 5369317
PMID: 28350381
DOI: 10.1038/sdata.2017.37

[…] From all genomes described here with completeness >10% and relevant GFMs and single-amplified genomes (SAGs) from the Integrated Microbial Genomes (IMG), ggKbase, and National Center for Biotechnology Information (NCBI) GenBank databases, phylogenetically informative marker genes were identified and extracted using the ‘tree’ command in CheckM. In Chec […]

library_books

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

2017
PMCID: 5520028
PMID: 28350393
DOI: 10.1038/ismej.2017.39

[…] scaffolds >1000 bp were binned by a combination of phylogenetic profiles, read coverage and nucleotide content (that is, GC proportion and tetranucleotide signatures) within the binning interface of ggKbase (http://ggkbase.berkeley.edu/) and by using emergent self-organizing maps constructed separately from tetranucleotide frequencies and coverage of the scaffolds across the nine different assemb […]

library_books

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

2017
MBio
PMCID: 5358914
PMID: 28223457
DOI: 10.1128/mBio.01969-16

[…] identified rRNA sequences with Infernal () by searching against databases from the SSU-Align package () and tRNAs with tRNAscan_SE (). Genome binning was carried out with the online interface within ggKbase as described previously () (http://ggkbase.berkeley.edu/). This method takes into account the phylogenetic profile, GC content, and coverage information. The completeness of bacterial bins was […]

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ggKbase institution(s)
Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA; School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA, USA; Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA; VA Palo Alto Health Care System, Palo Alto, CA, USA
ggKbase funding source(s)
Supported in part by NIH Grant 1R01AI092531-01, an EMBO long term fellowship, the Walter & Idun Berry Foundation, and the March of Dimes Foundation Research Grant 5-FY10-103, a Distinguished Clinical Scientist Award from the Doris Duke Charitable Trust, by NIH Pioneer Award DP1OD000964, and by the Thomas C. and Joan M. Merigan Endowment at Stanford University.

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