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MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

David Vallenet, Eugeni Belda, Alexandra Calteau, Stéphane Cruveiller, Stefan Engelen, Aurélie Lajus, François Le Fèvre, Cyrille Longin, Damien Mornico, David Roche, Zoé Rouy, Gregory Salvignol (+4 others)
2012 Nucleic Acids Research  
They also thank the entire system network team of Genoscope for its essential contribution to the efficiency of the platform, and Antoine Danchin for his careful editing of the manuscript.  ...  ACKNOWLEDGEMENTS The authors would like to thank all MaGe users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ...  MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. NUCLEIC ACIDS RESEARCH, 41 (D1), pp.E636-E647. https://doi.org/10.1093/nar/  ... 
doi:10.1093/nar/gks1194 pmid:23193269 pmcid:PMC3531135 fatcat:inrau5amu5btxjbw2ykwehkfny

MicroScope: a platform for microbial genome annotation and comparative genomics

D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury, A. Lajus, Z. Rouy, D. Roche, G. Salvignol, C. Scarpelli, C. Médigue
2009 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors would like to thank all MaGe users for their feedback that helped greatly in optimizing and improving many functionalities of the system.  ...  The authors thank the entire system network team of Genoscope for its essential contribution to the efficiency of the platform. Conflict of interest statement: None declared.  ...  Our system is currently being used for the genome analysis and curation of over 140 microbial genomes.  ... 
doi:10.1093/database/bap021 pmid:20157493 pmcid:PMC2790312 fatcat:3n3cu7s5mvazzk5n4go46hsipi

MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

2017 Briefings in Bioinformatics  
The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative  ...  In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data.  ...  Acknowledgements The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
doi:10.1093/bib/bbx113 pmid:28968784 pmcid:PMC6931091 fatcat:3kbei6onubhe3cobdiuk72xt4a

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoe Rouy, David Roche, Claude Scarpelli (+1 others)
2016 Nucleic Acids Research  
Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management  ...  Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations  ...  ACKNOWLEDGEMENTS The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
doi:10.1093/nar/gkw1101 pmid:27899624 pmcid:PMC5210572 fatcat:tpk2vklznzeuroyna7s62kanm4

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

2019 Nucleic Acids Research  
To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019).  ...  Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic  ...  ACKNOWLEDGEMENTS The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
doi:10.1093/nar/gkz926 pmid:31647104 pmcid:PMC7145621 fatcat:dwdxeaytnvar7iq3kudicrcz2q

Databases for Microbiologists: TABLE 1

Igor B. Zhulin, W. W. Margolin
2015 Journal of Bacteriology  
They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways.  ...  The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.  ...  Work in my laboratory is supported by grants GM072285 and DE024463 from the National Institutes of Health.  ... 
doi:10.1128/jb.00330-15 pmid:26013493 pmcid:PMC4505447 fatcat:6eyuvuplzjc7ravlhhmk6isg6i

Genome (re-)annotation and open-source annotation pipelines

Roland J. Siezen, Sacha A. F. T. Van Hijum
2010 Microbial Biotechnology  
Acknowledgements This project was carried out within the research programmes of the Kluyver Centre for Genomics of Industrial Fermentation and the Netherlands Bioinformatics Centre, which are part of the  ...  Netherlands Genomics Initiative/Netherlands Organization for Scientific Research.  ...  database http://img.jgi.doe.gov Markowitz et al. (2006); Markowitz et al. (2010) Microbes Online Virtual Institute for Microbial Stress and Survival An integrated portal for comparative and  ... 
doi:10.1111/j.1751-7915.2010.00191.x pmid:21255336 pmcid:PMC3815804 fatcat:6qxapk4bsre5jfbjq4onjphcre

INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

Intikhab Alam, André Antunes, Allan Anthony Kamau, Wail Ba alawi, Manal Kalkatawi, Ulrich Stingl, Vladimir B. Bajic, Enrique Hernandez-Lemus
2013 PLoS ONE  
Results: We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes.  ...  Conclusions: We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial  ...  Authors are also thankful to David Kamanda Ngugi and Mamoon Rashid from the Red Sea Center at KAUST for their help in testing the INDIGO system and to Arturo Magaña Mora for designing the INDIGO logo.  ... 
doi:10.1371/journal.pone.0082210 pmid:24324765 pmcid:PMC3855842 fatcat:wp5wxxqwcnb7vdf4ffwki6ho5i

A Comparison of Microbial Genome Web Portals

Peter D. Karp, Natalia Ivanova, Markus Krummenacker, Nikos Kyrpides, Mario Latendresse, Peter Midford, Wai Kit Ong, Suzanne Paley, Rekha Seshadri
2019 Frontiers in Microbiology  
Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists.  ...  , and large amount of curated data.  ...  We thank Maulik Shukla of Argonne National Laboratory and the University of Chicago and Rebecca Wattam of Virginia Tech for comments and corrections regarding PATRIC.  ... 
doi:10.3389/fmicb.2019.00208 pmid:30853946 pmcid:PMC6395428 fatcat:lefxs2tduvdtpasalfebkozm7u

Metabolic network modeling of microbial communities

Matthew B. Biggs, Gregory L. Medlock, Glynis L. Kolling, Jason A. Papin
2015 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
manual curation, and novel algorithms for integrating omics data and engineering communities.  ...  Genome-scale metabolic network reconstructions and constraint-based analysis are powerful methods that have the potential to make functional predictions about microbial communities.  ...  A simple workflow for genome-scale metabolic network reconstruction and accompanying constraint-based analysis The process begins with an annotated genome.  ... 
doi:10.1002/wsbm.1308 pmid:26109480 pmcid:PMC4575871 fatcat:xy2brs6dzvcupac6ywnipm5fgy

MaGe: a microbial genome annotation system supported by synteny results

D. Vallenet
2006 Nucleic Acids Research  
a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple  ...  In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria).  ...  ACKNOWLEDGEMENTS The authors would like to thank all MaGe users for their feedback that helped greatly in optimizing and improving many functionalities of the system.  ... 
doi:10.1093/nar/gkj406 pmid:16407324 pmcid:PMC1326237 fatcat:oz7zolxsvfhs7mmxbytw5ggd5y

Improving Microbial Genome Annotations in an Integrated Database Context

I-Min A. Chen, Victor M. Markowitz, Ken Chu, Iain Anderson, Konstantinos Mavromatis, Nikos C. Kyrpides, Natalia N. Ivanova, John Parkinson
2013 PLoS ONE  
Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data.  ...  We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems  ...  their contribution to the development and maintenance of the IMG systems.  ... 
doi:10.1371/journal.pone.0054859 pmid:23424620 pmcid:PMC3570495 fatcat:bio2te2hhvhjzfxufl5ej2exoi

The 27th annual Nucleic Acids Research database issue and molecular biology database collection

Daniel J Rigden, Xosé M Fernández
2019 Nucleic Acids Research  
PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser.  ...  hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools.  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva, especially, and the rest of the Oxford University Press team led by Joanna Ventikos for their help in compiling this issue.  ... 
doi:10.1093/nar/gkz1161 pmid:31906604 pmcid:PMC6943072 fatcat:2dx37pg3krcs5hamrlmgyb4h5e

Updates in Rhea—a manually curated resource of biochemical reactions

Anne Morgat, Kristian B. Axelsen, Thierry Lombardot, Rafael Alcántara, Lucila Aimo, Mohamed Zerara, Anne Niknejad, Eugeni Belda, Nevila Hyka-Nouspikel, Elisabeth Coudert, Nicole Redaschi, Lydie Bougueleret (+3 others)
2014 Nucleic Acids Research  
Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models.  ...  Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB  ...  exchanges and expert curation of the ChEBI entries essential for Rhea.  ... 
doi:10.1093/nar/gku961 pmid:25332395 pmcid:PMC4384025 fatcat:rg4drak3onguteit2c7wovb7wy

Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway

Valérie de Crécy-Lagard
2014 Computational and Structural Biotechnology Journal  
Comparing THF pathway reconstructions and functional annotations of a chosen set of folate synthesis genes in specific prokaryotes revealed the strengths and weaknesses of different microbial annotation  ...  This analysis revealed that most current platforms fail in metabolic reconstruction of variant pathways.  ...  Resource Integration Center (PATRIC); Kyoto Encyclopedia of Genes and Genomes (KEGG); Comprehensive Microbial Resource (CMR).  ... 
doi:10.1016/j.csbj.2014.05.008 pmid:25210598 pmcid:PMC4151868 fatcat:kqaw67neyvgifm3v7tcscmxb7e
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