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Protocols

GGDC specifications

Information


Unique identifier OMICS_17873
Name GGDC
Alternative name Genome-To-Genome Distance Calculator
Interface Web user interface
Restrictions to use None
Input format FASTA format
Computer skills Basic
Version 2.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline Markus Goker

Publications for Genome-To-Genome Distance Calculator

GGDC citations

 (242)
call_split

Draft Genome Sequences of Plant Associated Bacillus Strains Isolated from the Qinghai Tibetan Plateau

2018
Genome Announc
PMCID: 5946045
PMID: 29748403
DOI: 10.1128/genomeA.00375-18
call_split See protocol

[…] erage of the obtained scaffolds was 45× on average. Scaffolds were submitted to GenBank for gene annotation, which was implemented using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (). The genome-to-genome-distance calculator (GGDC) version 2.1 provided by DSMZ (http://ggdc.dsmz.de) was used for genome-based species delineation. Formula 2, which is especially appropriate to analyze draf […]

library_books

Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen driven thermophilic microbial community

2018
Sci Rep
PMCID: 5928048
PMID: 29712968
DOI: 10.1038/s41598-018-25146-9

[…] p://www.compgen.org/tools/PRED-TAT/) and the transmembrane helices with TMHMM Server v. 2.0 (http://www.cbs.dtu.dk/services/TMHMM/).The values of DNA-DNA hybridization in silico were calculated using GGDC 2, available at http://ggdc.dsmz.de/. […]

library_books

A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars

2018
Front Microbiol
PMCID: 5934430
PMID: 29755434
DOI: 10.3389/fmicb.2018.00805

[…] the number of predicted CDS. Furthermore, the genomes were compared by the Average Nucleotide Identity (ANI) and the in silico DNA-DNA hybridization (isDDH) indices using OrthoANI (Lee et al., ) and Genome-to-Genome Distance Calculator software (Meier-Kolthoff et al., ), respectively.Additionally, a phylogenetic analysis of the 13 genomes (LMG 24291T, LMG 10229T, LMG 9861, L397-L401, L406, LMG 90 […]

call_split

Draft Genome Sequence of Mycobacterium porcinum CSURP1564

2018
Genome Announc
PMCID: 5908923
PMID: 29674548
DOI: 10.1128/genomeA.00291-18
call_split See protocol

[…] coding genes, and 65 RNA genes, including 58 tRNAs, 3 rRNA operons, and 1 transfer-messenger RNA. The M. porcinum CSURP1564 genome was incorporated into in silico DNA-DNA hybridization (DDH) () using GGDC version 2.0 (), with reference genomes selected on the basis of the 16S rRNA gene sequence. This yielded 99.7% sequence similarity with M. porcinum IP141460001 (GenBank accession number MVIG00000 […]

library_books

Draft Genome Sequence of “Nocardia suismassiliense” Strain S 137 (CSUR P4007)

2018
Genome Announc
PMCID: 5908941
PMID: 29674534
DOI: 10.1128/genomeA.00212-18

[…] match with 99% similarity.Based on the 16S rRNA gene sequence proximity, genomes were selected and incorporated into in silico DNA-DNA hybridization (DDH) (). The DDH values were calculated using the Genome-to-Genome Distance Calculator (GGDC) version 2.0 online tool (). This analysis yielded 31.2% sequence similarity with the type strain N. tenerifensis NBRC 101015 (NCBI reference sequence NZ_BAG […]

library_books

Strategies for high altitude adaptation revealed from high quality draft genome of non violacein producing Janthinobacterium lividum ERGS5:01

2018
Stand Genomic Sci
PMCID: 5909252
PMID: 29721151
DOI: 10.1186/s40793-018-0313-3

[…] of two clusters among J. lividum strains was based on possession of vioABCDE operons. We then performed whole genome sequence-based in silico DDH using the online genome-to-genome calculator with the GGDC 2.0 BLAST+ model [] and ANI using nucleotide fasta sequences of each genome compared to the genome of strain ERGS5:01 as a reference with the Perl script []. The observed DDH value was 95.15% and […]

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GGDC institution(s)
Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; Eberhard-Karls-Universitat, Tubingen, Germany
GGDC funding source(s)
This work was supported by Zentrum fur Datenverarbeitung, University of Tubingen.

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