WebMGA 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


Add your version

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 IN pipelines

 (4)
2018
PMCID: 5790007
PMID: 29382867
DOI: 10.1038/s41598-018-20135-4

[…] 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., sequence alignments and genome content […]

2017
PMCID: 5331489
PMID: 28183779
DOI: 10.1128/genomeA.01307-16

[…] (https://github.com/lmrodriguezr/enveomics-gui), according to liu et al. (6). the rasttk pipeline (10) and patric (11) were used for genome annotation and comparative analysis. additionally, webmga (12) was used for cog annotation., the above-described process resulted in a cyanobacterial metagenome bin, namely, “ca. synechococcus spongiarum” m9. this genome consists of 179 contigs […]

2017
PMCID: 5423683
PMID: 28486484
DOI: 10.1371/journal.pone.0177278

[…] of transcription., selected genes based on differential expression and rpkm results were annotated in detail by several approaches. first, pfam, kog and go annotation was performed by means of webmga [21] and the blast2go freeware version 3.1.3. [22] using default settings. in addition, these genes were screened for cazymes by applying dbcan [23]. for the identification of cytochrome p450 […]

2015
PMCID: 4359502
PMID: 25887946
DOI: 10.1186/s12864-015-1350-6

[…] t trees [44]., protein functions were predicted by using rpsblast program against cog database of prokaryotic proteins and metabolic pathways were predicted by blast search against kegg database, via webmga server [45]., codon usage distances between core gene sets of all genomes were calculated using the formula:\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} […]

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).

WebMGA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review WebMGA