The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.

Szczegóły
Abstrakt

Tytuł:: The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.
Autorzy:: Chen IA; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Chu K; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Palaniappan K; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Ratner A; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Huang J; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Huntemann M; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Hajek P; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Ritter S; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Varghese N; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Seshadri R; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Roux S; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Woyke T; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Eloe-Fadrosh EA; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Ivanova NN; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Kyrpides NC; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Źródło:: Nucleic acids research [Nucleic Acids Res] 2021 Jan 08; Vol. 49 (D1), pp. D751-D763.
Typ publikacji:: Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
Język:: English
Imprint Name(s):: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:: Data Analysis*
Data Management*
Databases, Genetic*
Genome, Archaeal*
Genome, Microbial*
Metagenome ; RNA, Ribosomal, 16S/genetics ; Search Engine
References:: Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432. (PMID: 30357350)
Nat Rev Microbiol. 2020 Jun;18(6):313-314. (PMID: 32350400)
Nucleic Acids Res. 2019 Jan 8;47(D1):D490-D494. (PMID: 30445555)
Nat Biotechnol. 2018 Apr;36(4):359-367. (PMID: 29553575)
mSystems. 2021 May 18;6(3):. (PMID: 34006627)
Genome Res. 2011 Mar;21(3):487-93. (PMID: 21209072)
Nucleic Acids Res. 2018 Jan 4;46(D1):D493-D496. (PMID: 29040681)
Nucleic Acids Res. 2017 Jan 4;45(D1):D560-D565. (PMID: 27903896)
Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204. (PMID: 29905871)
Nucleic Acids Res. 2016 Jan 4;44(D1):D471-80. (PMID: 26527732)
Genome Res. 2018 Jul;28(7):1079-1089. (PMID: 29773659)
Nucleic Acids Res. 2019 Jan 8;47(D1):D649-D659. (PMID: 30357420)
Nucleic Acids Res. 2019 Jan 8;47(D1):D280-D284. (PMID: 30398663)
BMC Bioinformatics. 2010 Mar 08;11:119. (PMID: 20211023)
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4. (PMID: 15608160)
Bioinformatics. 2001 Jul;17(7):646-53. (PMID: 11448883)
Nat Protoc. 2007;2(4):953-71. (PMID: 17446895)
Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):358-366. (PMID: 30622213)
Dev Growth Differ. 2019 Jun;61(5):316-326. (PMID: 31037722)
BMC Bioinformatics. 2007 Jun 18;8:209. (PMID: 17577412)
Nucleic Acids Res. 2019 Jan 8;47(D1):D678-D686. (PMID: 30407573)
Science. 1991 Nov 29;254(5036):1374-7. (PMID: 1962196)
Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9. (PMID: 25428365)
Nucleic Acids Res. 2015 Aug 18;43(14):6761-71. (PMID: 26150420)
Biometrika. 1947;34(1-2):28-35. (PMID: 20287819)
Nucleic Acids Res. 2013 Jan;41(Database issue):D387-95. (PMID: 23197656)
Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361. (PMID: 27899662)
Stand Genomic Sci. 2015 Oct 26;10:86. (PMID: 26512311)
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21. (PMID: 21062823)
Stand Genomic Sci. 2014 Feb 15;9(3):599-601. (PMID: 25197446)
Nucleic Acids Res. 2020 Jan 8;48(D1):D422-D430. (PMID: 31665416)
Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677. (PMID: 30289528)
Genome Res. 2015 Jul;25(7):1043-55. (PMID: 25977477)
Bioinformatics. 2009 May 15;25(10):1335-7. (PMID: 19307242)
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096. (PMID: 34417604)
Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89. (PMID: 26542840)
Nat Biotechnol. 2018 Jul 6;36(7):566-569. (PMID: 29979655)
Bioinformatics. 2019 Nov 15;:. (PMID: 31730192)
Front Microbiol. 2019 Feb 22;10:208. (PMID: 30853946)
Bioinformatics. 2013 Nov 15;29(22):2933-5. (PMID: 24008419)
PeerJ. 2015 Aug 27;3:e1165. (PMID: 26336640)
Nucleic Acids Res. 2018 Jan 4;46(D1):D41-D47. (PMID: 29140468)
Substance Nomenclature:: 0 (RNA, Ribosomal, 16S)
Entry Date(s):: Date Created: 20201029 Date Completed: 20210126 Latest Revision: 20240330
Update Code:: 20240330
PubMed Central ID:: PMC7778900
DOI:: 10.1093/nar/gkaa939
PMID:: 33119741
: Czasopismo naukowe

Full Text Finder

The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) contains annotated isolate genome and metagenome datasets sequenced at the DOE's Joint Genome Institute (JGI), submitted by external users, or imported from public sources such as NCBI. IMG v 6.0 includes advanced search functions and a new tool for statistical analysis of mixed sets of genomes and metagenome bins. The new IMG web user interface also has a new Help page with additional documentation and webinar tutorials to help users better understand how to use various IMG functions and tools for their research. New datasets have been processed with the prokaryotic annotation pipeline v.5, which includes extended protein family assignments.
(Published by Oxford University Press on behalf of Nucleic Acids Research 2020.)

Informacja