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Protocols

WebMGA specifications

Information


Unique identifier OMICS_01524
Name WebMGA
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Weizhong Li

Information


Unique identifier OMICS_01524
Name WebMGA
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Weizhong Li

Publication for WebMGA

WebMGA citations

 (94)
library_books

Lineageā€specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group

2018
Mol Ecol
PMCID: 5947300
PMID: 29509989
DOI: 10.1111/mec.14546

[…] ampling information, but these genomes were included to provide as much information as possible on the genomic diversity within the Bacillus group (TableĀ ). Functional predictions were made using the WebMGA COG server using rpsblast 2.2.15 on the NCBI COG database (http://weizhong-lab.ucsd.edu/metagenomic-analysis/server/cog/). Sequence type (ST) assignment from assembled genome sequences was perf […]

library_books

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites

2018
PLoS One
PMCID: 5874029
PMID: 29590215
DOI: 10.1371/journal.pone.0194487

[…] ukaryota_odb9 data set was carried out []. Gene annotation, in an automated fashion, was carried out using interproscan [, ]. Eukaryotic orthologous group (KOG) assignments were carried out using the WebMGA site (http://weizhong-lab.ucsd.edu/metagenomic-analysis/) with default settings []. The genome sequence and raw genome / transcriptome reads of K. bialata were deposited under DDBJ BioProject P […]

call_split

Comparative Genomics and Identification of an Enterotoxin Bearing Pathogenicity Island, SEPI 1/SECI 1, in Staphylococcus epidermidis Pathogenic Strains

2018
Toxins
PMCID: 5869381
PMID: 29495323
DOI: 10.3390/toxins10030093
call_split See protocol

[…] ative proteins encoded by the SE90 and SE95 genomes, were compared with all other strains using the Clusters of Orthologous Groups of proteins (COGs) database. COG categories were retrieved using the WebMGA software platform (Center for Research in Biological Systems, University of California San Diego, California, USA), with an e-value cut-off of 0.001 for prediction [,]. […]

library_books

Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease

2018
Sci Rep
PMCID: 5790007
PMID: 29382867
DOI: 10.1038/s41598-018-20135-4

[…] ned in all genomes from this study. Functional annotation of the list was made using RPSBLAST 2.2.15 program on the Clusters of Orthologous Groups (COG) database (NCBI, 28/03/2017) implemented in the WebMGA server (http://weizhong-lab.ucsd.edu/metagenomic-analysis/server/cog/). A total of 2,639/4,798 (55%) genes could be assigned to a described COG. […]

library_books

The dynamic intein landscape of eukaryotes

2018
Mob DNA
PMCID: 5784728
PMID: 29416568
DOI: 10.1186/s13100-018-0111-x

[…] erPro protein analysis tool (www.ebi.ac.uk/interpro/). KOG annotation for nuclear (nDNA) and viral (vDNA) inteins was performed using protein function annotation by the KOG database tool available at WebMGA server [, ] (weizhong-lab.ucsd.edu/metagenomic-analysis/); COG annotation for inteins from chloroplast genomes (cpDNA) was performed using the COG database [] (www.ncbi.nlm.nih.gov/COG/). The e […]

library_books

Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1

2017
Stand Genomic Sci
PMCID: 5738896
PMID: 29276572
DOI: 10.1186/s40793-017-0301-z

[…] dant protein sequences. To identify RNA genes, RNAmmer v1.2 [] (rRNAs) and tRNAscan-SE [] (tRNAs) were used. Clusters of Orthologous Groups assignments and Pfam domain predictions were done using the WebMGA server []. Transmembrane helices were predicted with TMHMM [] and Phobius []. For signal peptide prediction, SignalP 4.1 [] was used. CRISPRFinder [] was used to detect Clustered Regularly Inte […]

Citations

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WebMGA institution(s)
Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
WebMGA funding source(s)
This study was supported by Award R01HG005978 from the National Human Genome Research Institute (NHGRI) and Award R01RR025030 from National Center for Research Resources (NCRR).

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