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MetaMine - A tool to detect and analyse gene patterns in their environmental context
2008
BMC Bioinformatics
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Results: MetaMine is an interactive data mining tool which enables the detection of gene patterns in an environmental context. ...
Prevailing biological processes associated with a key gene can be used to infer new annotations and shape hypotheses to guide further analyses. ...
Acknowledgements We thank the reviewers for their useful comments to improve the manuscript and all MetaFunctions partners for fruitful discussions. ...
doi:10.1186/1471-2105-9-459
pmid:18957118
pmcid:PMC2615450
fatcat:ssxpmk52hja53fawaoulciy57e
Linking genomics and metabolomics to chart specialized metabolic diversity
2020
Chemical Society Reviews
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In recent years, genomic and metabolomic analyses of specialized metabolic diversity have been scaled up to study thousands of samples simultaneously. ...
Also referred to as natural products, they have been widely applied in medicine, agriculture, cosmetic and food industries. ...
To analyse substructures in context of metabolite diversity, annotations from MS2LDA can be used to annotate molecular networks; the MolNetEnhancer software facilitates this (Fig. 2e) 34 and thereby ...
doi:10.1039/d0cs00162g
pmid:32393943
fatcat:jjkyiefpsrdr5lpj5f6jjyyxnm
Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds
2020
Biomolecules
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Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. ...
Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches ...
The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ...
doi:10.3390/biom10050673
pmid:32349314
fatcat:3epphp4ucbbbpdpzhxubqlvbwe
A Primer on Metagenomics
2010
PLoS Computational Biology
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From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. ...
In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. ...
We would also like to thank the referees for contributing their time and effort towards making this a better article. IF dedicates his contribution to the memory of Ilan Friedberg. ...
doi:10.1371/journal.pcbi.1000667
pmid:20195499
pmcid:PMC2829047
fatcat:ykwqb3r4preo7is4vcqlk2caey
COMPUTATIONAL TOOLS FOR THE SECONDARY ANALYSIS OF METABOLOMICS EXPERIMENTS
2013
Computational and Structural Biotechnology Journal
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Introduction Over the past decade metabolomics has emerged as a powerful tool used in a variety of quite diverse fields for hypothesis development, to elaborate unknown gene functions, biomarker discovery ...
As metabolomics remains a developing field, bioinformatic tools designed to perform this task continue to be developed and released by various groups using diverse algorithms. ...
For the purposes of combined analyses there is a p-value calculated separately for genes and metabolites as well as a combined value. ...
doi:10.5936/csbj.201301003
pmid:24688685
pmcid:PMC3962093
fatcat:4zfhlfrvjnhzhbdzgx6dh63cpe
Chemical, Physiological and Metabolic Interactions between Pseudomonas, Metals and Environmental Nutrients
[article]
2017
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These results provide new insight into the interactions between a bacterium and the nutrients and stressors in their environment. ...
By deleting genes that were expected to be involved in energy-taxis, a process that allows bacteria to swim to metabolizable carbon sources, I found that this was not how KF707 swims towards biphenyl. ...
For the purposes of combined analyses there is a p-value calculated separately for genes and metabolites as well as a combined value. ...
doi:10.11575/prism/25315
fatcat:zf746n56hzfd7pvjbu3xkc7dgm