MOSGA 2: Comparative genomics and validation tools.
Comparative genomics
Framework
Genome annotation
Phylogenetics
Pipeline
Quality control
Workflow
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2021
2021
Historique:
received:
10
08
2021
revised:
23
09
2021
accepted:
24
09
2021
entrez:
29
10
2021
pubmed:
30
10
2021
medline:
30
10
2021
Statut:
epublish
Résumé
Due to the highly growing number of available genomic information, the need for accessible and easy-to-use analysis tools is increasing. To facilitate eukaryotic genome annotations, we created MOSGA. In this work, we show how MOSGA 2 is developed by including several advanced analyses for genomic data. Since the genomic data quality greatly impacts the annotation quality, we included multiple tools to validate and ensure high-quality user-submitted genome assemblies. Moreover, thanks to the integration of comparative genomics methods, users can benefit from a broader genomic view by analyzing multiple genomic data sets simultaneously. Further, we demonstrate the new functionalities of MOSGA 2 by different use-cases and practical examples. MOSGA 2 extends the already established application to the quality control of the genomic data and integrates and analyzes multiple genomes in a larger context, e.g., by phylogenetics.
Identifiants
pubmed: 34712396
doi: 10.1016/j.csbj.2021.09.024
pii: S2001-0370(21)00409-8
pmc: PMC8517542
doi:
Types de publication
Journal Article
Langues
eng
Pagination
5504-5509Informations de copyright
© 2021 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
Bioinformatics. 2007 Nov 1;23(21):2947-8
pubmed: 17846036
Mol Biol Evol. 2015 Oct;32(10):2798-800
pubmed: 26130081
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Bioinformatics. 2019 Feb 1;35(3):526-528
pubmed: 30016406
PLoS Comput Biol. 2020 Oct 15;16(10):e1008259
pubmed: 33057327
Cell. 2019 Dec 12;179(7):1623-1635.e11
pubmed: 31835036
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W465-7
pubmed: 15980513
G3 (Bethesda). 2020 Jun 1;10(6):1829-1836
pubmed: 32317270
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811
pubmed: 30395283
Nat Commun. 2018 Nov 30;9(1):5114
pubmed: 30504855
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32761142
Nat Biotechnol. 2017 Nov;35(11):1026-1028
pubmed: 29035372
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Sci Data. 2018 Sep 04;5:180154
pubmed: 30179231
Curr Biol. 2020 Jun 22;30(12):2312-2320.e5
pubmed: 32413308
Nucleic Acids Res. 2019 Jul 2;47(W1):W191-W198
pubmed: 31066453
Cell Host Microbe. 2019 May 8;25(5):656-667.e8
pubmed: 31028005
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Nucleic Acids Res. 2013 Jan;41(Database issue):D377-86
pubmed: 23193289
Nature. 2018 Apr;556(7701):339-344
pubmed: 29643504
Trends Ecol Evol. 2014 May;29(5):252-9
pubmed: 24726347
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
PLoS Biol. 2020 Dec 2;18(12):e3001007
pubmed: 33264284
Genome Biol. 2016 Apr 12;17:66
pubmed: 27072794
Bioinformatics. 2021 Apr 1;36(22-23):5514-5515
pubmed: 33258916
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613
pubmed: 30476243
Nucleic Acids Res. 2019 Jan 8;47(D1):D581-D589
pubmed: 30407591
Nat Commun. 2018 Nov 19;9(1):4881
pubmed: 30451857
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
Genome Res. 2012 Mar;22(3):557-67
pubmed: 22147368
Nucleic Acids Res. 2019 Jan 8;47(D1):D94-D99
pubmed: 30365038
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096
pubmed: 34417604
Genome Biol. 2020 Sep 10;21(1):244
pubmed: 32912302
Mol Ecol Resour. 2020 Sep;20(5):1361-1371
pubmed: 32419357
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
pubmed: 7984417
Mol Biol Evol. 2018 Mar 1;35(3):543-548
pubmed: 29220515
Brief Bioinform. 2017 Mar 1;18(2):179-182
pubmed: 26655251
Bioinformatics. 2004 Nov 1;20(16):2878-9
pubmed: 15145805
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Nat Biotechnol. 2017 Aug 8;35(8):725-731
pubmed: 28787424
BMC Bioinformatics. 2004 May 14;5:59
pubmed: 15144565
Sci Data. 2020 Jan 21;7(1):29
pubmed: 31964893