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METAGENassist specifications

Information


Unique identifier OMICS_07815
Name METAGENassist
Interface Web user interface
Restrictions to use None
Input format Users upload a taxonomic profile in one of several supported formats. A taxonomic profile file contains the names of microbial species (or other taxonomic classes) and their relative abundance in at least 2 samples. Accepted formats include CSV format, or data generated by mothur, QIIME, MG-RAST, MEGAN, and STAMP. Users will also benefit by uploading an optional file containing metadata for each sample (CSV format).
Output format Upon completion, METAGENassist generates a variety of well-annotated tables and colorful, labeled graphs in an anti-aliased PNG format. PDF versions for some plots are also available. The processed data and images are available for download.
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/METAGENassist

Maintainer


  • person_outline David Wishart

Publication for METAGENassist

METAGENassist citations

 (24)
library_books

In feed bambermycin medication induces anti inflammatory effects and prevents parietal cell loss without influencing Helicobacter suis colonization in the stomach of mice

2018
PMCID: 5894178
PMID: 29636083
DOI: 10.1186/s13567-018-0530-1

[…] dissimilarity index. differences in functional profiles of gastric bacterial communities were analyzed by mapping taxa into several phenotypes (i.e. metabolism, gram staining, sporulation,…) using metagenassist® []. only the phenotypes detected in more than 50% of the samples were included for further analysis., statistical analysis was performed using spss statistics 24® (ibm, new york, usa). […]

library_books

Exploring Viral Diversity in a Unique South African Soil Habitat

2018
Sci Rep
PMCID: 5758573
PMID: 29311639
DOI: 10.1038/s41598-017-18461-0

[…] phylogenetic trees were based on the reference sequences and the kogelberg biosphere reserve virome sequences, and computed with 100 bootstraps. further analysis of the sequences was performed using metagenassist (a web server that provides a broad range of statistical tools for comparative metagenomics). functional assignments produced by virome using 120 identified functional subsystems […]

library_books

Hypersaline sapropels act as hotspots for microbial dark matter

2017
Sci Rep
PMCID: 5522462
PMID: 28733590
DOI: 10.1038/s41598-017-06232-w

[…] to closed-reference otu-picking compared to using all the available read data for each study. taxonomic-to-phenotypic mapping was performed by linking otus nomenclature to taxonomic assignments in metagenassist. the graphical representation of the phenotipic cladogram was constructed with graphlan software., all sequence data are available through the national center for biotechnology […]

library_books

Subventricular zone involvement in Glioblastoma – A proteomic evaluation and clinicoradiological correlation

2017
Sci Rep
PMCID: 5431125
PMID: 28469129
DOI: 10.1038/s41598-017-01202-8

[…] to identify the pathways affected in the sub groups of gbm patients., itraq data for the tissue proteomic analysis of svz−, svz+ gbm tumors and normal/control tissues was subjected to plsda using metagenassist, an online tool. both svz− and svz+ gbms were segregated from each other on a 3d-score plot obtained from this multivariate analysis., hemopexin levels in gbm patient (both svz+ […]

library_books

Stable mucus associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas

2017
Sci Rep
PMCID: 5374439
PMID: 28361923
DOI: 10.1038/srep45362

[…] when the ratio of mean sequence counts in mucus over water samples was <1., functional differences based on bacterial 16s community composition (otu taxonomy and abundance), were assessed with metagenassist. input files were created in mothur using the ‘make.shared’ and ‘classify.otu’ commands based on all coral samples. 1,978 distinct otus were assigned, mapped, condensed into 500 […]

library_books

Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt infested fields in Central America

2017
Sci Rep
PMCID: 5366900
PMID: 28345666
DOI: 10.1038/srep45318

[…] plants, a reduced otu table was normalized at 19,892 reads. the core microbiome was defined as those otus at a dissimilarity level of 3% that were present in at least 50% of the respective samples. metagenassist was employed to visualize co-occurrence patterns of taxa within the normalized core microbiome based on spearman’s rank correlation. for visualizing relationships, core otus […]


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METAGENassist institution(s)
Department of Computing Science, University of Alberta, Edmonton, AB, Canada

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