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MetaMine - A tool to detect and analyse gene patterns in their environmental context

Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann, Frank O Glockner
2008 BMC Bioinformatics  
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

Justin J J van der Hooft, Hosein Mohimani, Anelize Bauermeister, Pieter C Dorrestein, Katherine R Duncan, Marnix H Medema
2020 Chemical Society Reviews  
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

Kattia Núñez-Montero, Damián Quezada-Solís, Zeinab G. Khalil, Robert J. Capon, Fernando D. Andreote, Leticia Barrientos
2020 Biomolecules  
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

John C. Wooley, Adam Godzik, Iddo Friedberg, Philip E. Bourne
2010 PLoS Computational Biology  
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

Sean C. Booth, Aalim M. Weljie, Raymond J. Turner
2013 Computational and Structural Biotechnology Journal  
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]

Sean C. Booth, University Of Calgary, University Of Calgary, Raymond J. Turner
2017
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