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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.  ...  In the context of the French National Sequencing Center (CEA/DSV/Institut de Gé nomique/Genoscope), we have developed a platform, named MicroScope, to support microbial genome (re)annotation and comparative  ... 
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  ...  Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical.  ...  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  
The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.  ...  Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions.  ...  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

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.  ...  In contrast to organism-specific annotation systems reviewed in (2) , MicroScope enables curation in a rich comparative genomic and metabolic context, the annotated genome being compared with all public  ... 
doi:10.1093/nar/gks1194 pmid:23193269 pmcid:PMC3531135 fatcat:inrau5amu5btxjbw2ykwehkfny

Under the microscope: From pathogens to probiotics and back

Roy D Sleator
2015 Bioengineered  
gastrointestinal tract; focusing first on the bacterial stress responses needed to overcome the physiochemical defenses of the host, specifically how these stress survival strategies can be used as targets for  ...  of novel vaccine and drug delivery platforms.  ...  This was followed by the functional analysis of bsh, pva, and btlBthree genes previously annotated as bile-associated loci in the public databases. 34 While deletion mutants revealed a role for all three  ... 
doi:10.1080/21655979.2015.1089368 pmid:26339986 pmcid:PMC4825842 fatcat:2uiubsiywjbbll3n5d74jvhejy

Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert, Israel

Nir Irit, Barak Hana, Kramarsky‐Winter Esti, Kushmaro Ariel, de los Ríos Asunción
2021 Environmental Microbiology  
This approach revealed extensive epilithic and endolithic colonization and close microbial-mineral interactions.  ...  Thus, our results provide evidence for the potential participation of the microorganisms colonizing these rocks during different solubilization and mineralization processes.  ...  Special thanks to Microscopy service from the MNCN (CSIC) for technical assistance and Isaac Garrido for lichen identification assistance.  ... 
doi:10.1111/1462-2920.15635 pmid:34110072 fatcat:ouuanimmb5ag3ndlwb5bircuqq

How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health

Vladimir Kuznetsov, Hwee Kuan Lee, Sebastian Maurer-Stroh, Maria Judit Molnár, Sandor Pongor, Birgit Eisenhaber, Frank Eisenhaber
2013 Health Information Science and Systems  
It remains a sad fact that many, if not most biomolecular mechanisms that translate the human genomic information into phenotypes are not known and, thus, most of the molecular and cellular data cannot  ...  Author summary: With DNA sequencing and computers becoming increasingly cheap and accessible to the layman, the idea of integrating biomolecular and clinical patient data seems to become a realistic, short-term  ...  Acknowledgements This work was partially supported by grants A*STAR-NKTH 10/1/06/24635, IAF311010, A*STAR IMAGIN and IAF311011 at the Singaporean side and by the grants TÉT 10-1-2011-0058 (bilateral cooperation  ... 
doi:10.1186/2047-2501-1-2 pmid:25825654 pmcid:PMC4336111 fatcat:gc34ee7fybfpvg646rftunfkje

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.  ...  Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis.  ...  ACKNOWLEDGMENTS I thank Michael Galperin, Nikos Kyrpides, and members of my laboratory for constructive criticism and many helpful suggestions.  ... 
doi:10.1128/jb.00330-15 pmid:26013493 pmcid:PMC4505447 fatcat:6eyuvuplzjc7ravlhhmk6isg6i

Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1

X. Wang, Q. Wang, W. Zhang, Y. Wang, L. Li, T. Wen, T. Zhang, Y. Zhang, J. Xu, J. Hu, S. Li, L. Liu (+7 others)
2014 Genome Announcements  
Compared to the reported draft sequence, extensive rearrangements and differences were found, indicating high genomic flexibility and "domestication" by accelerated evolution of the strain upon repeated  ...  We report the complete genomic sequence of Magnetospirillum gryphiswaldense MSR-1 (DSM 6361), a type strain of the genus Magnetospirillum belonging to the Alphaproteobacteria.  ...  ACKNOWLEDGMENTS This study was supported by the Chinese National Natural Science Foundation (grants 30970041 and 31270093).  ... 
doi:10.1128/genomea.00171-14 pmid:24625872 pmcid:PMC3953193 fatcat:wm26fspd7bgg7or5cxggyealsu

IBM Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale [article]

Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mary Roth, Vandana Mukherjee, James H. Kaufman
2020 arXiv   pre-print
In this paper, we describe IBM Functional Genomics Platform (formerly known as OMXWare), a comprehensive database relating genotype to phenotype for bacterial life.  ...  We describe the data selection, the pipeline to create and update the IBM Functional Genomics Platform, and the developer tools (Python SDK and REST APIs) which allow researchers to efficiently study microbial  ...  Haiminen and Dr. L. Parida of IBM Research for helpful discussion and insights into new applications of IBM Functional Genomics Platform.  ... 
arXiv:1911.02095v3 fatcat:bn6kssh2ezbqnashkxqzga3faq

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  ...  The THF biosynthesis pathway and enzymes are, however, not universal and alternate solutions are found for most steps, making this pathway a challenge to annotate automatically in many genomes.  ...  The steps from gene calling to function prediction have been streamlined in annotation platforms, allowing laboratories with little bioinformatics capacity to annotate microbial genomes in a short amount  ... 
doi:10.1016/j.csbj.2014.05.008 pmid:25210598 pmcid:PMC4151868 fatcat:kqaw67neyvgifm3v7tcscmxb7e

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.  ...  In addition to (curated) annotation information, a few databases also offer bioinformatics and/or visualisation tools for comparative genomics, e.g.  ... 
doi:10.1111/j.1751-7915.2010.00191.x pmid:21255336 pmcid:PMC3815804 fatcat:6qxapk4bsre5jfbjq4onjphcre

Decoding Complex Soil Microbial Communities through New Age "Omics"

Girish R Nair, Suresh SS Raja
2017 Journal of Microbial & Biochemical Technology  
In comparative genomics, genome of a pathogenic bacterium is compared with a non-pathogenic bacterium to identify molecular targets that can be manipulated for designing new drugs.  ...  Bacterial genomics has led to identification of putative gene products by a comparative approach called comparative genomics.  ... 
doi:10.4172/1948-5948.1000382 fatcat:3nrlzvoju5fqrfmmorr3saw63q

Complete Genome Sequences of Six Strains of the Genus Methylobacterium

C. J. Marx, F. Bringel, L. Chistoserdova, L. Moulin, M. Farhan Ul Haque, D. E. Fleischman, C. Gruffaz, P. Jourand, C. Knief, M.-C. Lee, E. E. L. Muller, T. Nadalig (+15 others)
2012 Journal of Bacteriology  
The complete and assembled genome sequences were determined for six strains of the alphaproteobacterial genus Methylobacterium, chosen for their key adaptations to different plant-associated niches and  ...  ACKNOWLEDGMENTS We are grateful to the JGI personnel who participated in the sequencing, assembly, and automated annotation processes.  ...  Additional automatic and manual sequence annotations, as well as comparative genome analysis, were performed using the MicroScope platform at Genoscope (16) .  ... 
doi:10.1128/jb.01009-12 pmid:22887658 pmcid:PMC3415506 fatcat:dbwhoj4iobhahe5p775asdyzxe
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