MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.
comparative genomics
gene function curation
metabolic networks
microbial genome annotation system
transcriptomics
variant detection
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
19 07 2019
19 07 2019
Historique:
received:
31
05
2017
revised:
17
07
2017
pubmed:
3
10
2017
medline:
11
4
2020
entrez:
3
10
2017
Statut:
ppublish
Résumé
The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. 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 analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. 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. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.
Identifiants
pubmed: 28968784
pii: 4157326
doi: 10.1093/bib/bbx113
pmc: PMC6931091
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1071-1084Informations de copyright
© The Author 2017. Published by Oxford University Press.
Références
Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542
pubmed: 27899627
Nucleic Acids Res. 2005 Oct 07;33(17):5691-702
pubmed: 16214803
Nucleic Acids Res. 2017 Jan 4;45(D1):D566-D573
pubmed: 27789705
Nucleic Acids Res. 2015 Jan;43(Database issue):D1064-70
pubmed: 25348399
Bioinformatics. 2012 Feb 15;28(4):464-9
pubmed: 22199388
Methods Mol Biol. 2007;396:31-41
pubmed: 18025684
Microbiology. 2013 Apr;159(Pt 4):757-770
pubmed: 23429746
Nat Chem Biol. 2015 Sep;11(9):625-31
pubmed: 26284661
Nucleic Acids Res. 2013 Jan;41(Database issue):D636-47
pubmed: 23193269
Nucleic Acids Res. 2016 Jan 4;44(D1):D574-80
pubmed: 26578574
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9
pubmed: 15980515
Genome Res. 2000 Aug;10(8):1074-7
pubmed: 10958625
Microbiology. 2009 Jun;155(Pt 6):1758-75
pubmed: 19383706
Nucleic Acids Res. 2003 Jul 1;31(13):3723-6
pubmed: 12824403
Biotechniques. 2003 Feb;34(2):374-8
pubmed: 12613259
Microb Comp Genomics. 2000;5(4):205-22
pubmed: 11471834
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169
pubmed: 27899622
BMC Genomics. 2016 Apr 26;17:307
pubmed: 27118214
Nat Biotechnol. 2008 May;26(5):541-7
pubmed: 18464787
Nucleic Acids Res. 2013 Jan;41(Database issue):D387-95
pubmed: 23197656
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D300-2
pubmed: 14681418
J Mol Biol. 2000 Mar 17;297(1):233-49
pubmed: 10704319
Brief Bioinform. 2016 Sep;17(5):877-90
pubmed: 26454094
Nucleic Acids Res. 2017 Apr 20;45(7):4279
pubmed: 27980062
Bioinformatics. 2006 Sep 15;22(18):2196-203
pubmed: 16837528
Nucleic Acids Res. 2016 Jan 4;44(D1):D471-80
pubmed: 26527732
BMC Bioinformatics. 2011 Apr 22;12:116
pubmed: 21513511
Nucleic Acids Res. 2006 Jan 10;34(1):53-65
pubmed: 16407324
Bioinformatics. 2009 May 1;25(9):1189-91
pubmed: 19151095
Database (Oxford). 2009;2009:bap021
pubmed: 20157493
Nucleic Acids Res. 2004 Oct 28;32(19):5766-79
pubmed: 15514110
Genome Biol Evol. 2013;5(1):233-42
pubmed: 23315380
PLoS Genet. 2009 Jan;5(1):e1000344
pubmed: 19165319
Nucleic Acids Res. 2016 Jan 4;44(D1):D646-53
pubmed: 26578582
Nucleic Acids Res. 2017 Jan 4;45(D1):D517-D528
pubmed: 27899624
Nucleic Acids Res. 2016 Jan 4;44(D1):D694-7
pubmed: 26578559
Environ Microbiol. 2016 Oct;18(10):3403-3424
pubmed: 26913973
Nucleic Acids Res. 2017 Jul 3;45(W1):W36-W41
pubmed: 28460038
J Clin Microbiol. 2014 May;52(5):1501-10
pubmed: 24574290
J Bacteriol. 2011 Mar;193(6):1461-72
pubmed: 21239590
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427