MaizeGDB 2018: the maize multi-genome genetics and genomics database.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2019
08 01 2019
Historique:
received:
13
09
2018
accepted:
16
10
2018
pubmed:
9
11
2018
medline:
19
5
2020
entrez:
9
11
2018
Statut:
ppublish
Résumé
Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly. Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding. MaizeGDB hosts a wide range of data including recent support of new data types including genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data (SNPversity), download and compare gene expression data (qTeller), visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user-specified queries to the MaizeGDB database (MaizeMine). MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible. MaizeGDB is accessible online at https://www.maizegdb.org.
Identifiants
pubmed: 30407532
pii: 5165183
doi: 10.1093/nar/gky1046
pmc: PMC6323944
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
D1146-D1154Références
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D393-7
pubmed: 14681441
Proc Natl Acad Sci U S A. 1928 Jan;14(1):69-75
pubmed: 16587308
Proc Natl Acad Sci U S A. 1931 Aug;17(8):492-7
pubmed: 16587654
Nucleic Acids Res. 2007 Jan;35(Database issue):D895-900
pubmed: 17202174
Genetics. 1932 Jul;17(4):481-501
pubmed: 17246663
Plant Cell. 2007 Jul;19(7):2091-4
pubmed: 17660357
Genetics. 2008 Jan;178(1):539-51
pubmed: 18202393
Plant J. 2008 Feb;53(4):661-73
pubmed: 18269575
Comp Funct Genomics. 2002;3(2):128-31
pubmed: 18628892
Trends Plant Sci. 2008 Aug;13(8):415-20
pubmed: 18650120
Int J Plant Genomics. 2008;2008:496957
pubmed: 18769488
Plant Physiol. 2009 Dec;151(4):1703-28
pubmed: 19926802
Science. 2009 Nov 20;326(5956):1115-7
pubmed: 19965431
Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.emo132
pubmed: 20147033
Database (Oxford). 2010 Jul 06;2010:baq007
pubmed: 20627860
J Exp Bot. 2011 Jun;62(10):3545-61
pubmed: 21402660
Database (Oxford). 2009;2009:bap020
pubmed: 21847242
Int J Plant Genomics. 2011;2011:373875
pubmed: 22220167
Int J Plant Genomics. 2011;2011:923035
pubmed: 22253616
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Bioinformatics. 2012 Dec 1;28(23):3163-5
pubmed: 23023984
Brief Bioinform. 2013 Mar;14(2):162-71
pubmed: 23376193
Database (Oxford). 2013 Apr 02;2013:bat016
pubmed: 23550062
Genome Biol. 2013 Jun 11;14(6):R55
pubmed: 23759205
Science. 2014 May 2;344(6183):510-3
pubmed: 24786077
Nat Commun. 2015 Apr 16;6:6914
pubmed: 25881062
PLoS One. 2015 Jun 19;10(6):e0126185
pubmed: 26090679
Nucleic Acids Res. 2016 Jan 4;44(D1):D1195-201
pubmed: 26432828
Brief Bioinform. 2016 Sep;17(5):877-90
pubmed: 26454094
Methods Mol Biol. 2016;1374:187-202
pubmed: 26519406
PLoS Genet. 2015 Nov 17;11(11):e1005670
pubmed: 26575831
Science. 2016 Aug 19;353(6301):814-8
pubmed: 27540173
Plant Cell. 2016 Nov;28(11):2700-2714
pubmed: 27803309
Plant Genome. 2016 Mar;9(1):
pubmed: 27898762
BMC Syst Biol. 2016 Nov 29;10(1):129
pubmed: 27899149
Database (Oxford). 2017 Jan 1;2017:
pubmed: 28605768
Nat Commun. 2017 Nov 30;8(1):1874
pubmed: 29187731
Database (Oxford). 2018 Jan 1;2018:
pubmed: 29688387
Nat Genet. 2018 Sep;50(9):1289-1295
pubmed: 30061735
Nat Genet. 2018 Sep;50(9):1282-1288
pubmed: 30061736
Database (Oxford). 2018 Jan 1;2018:
pubmed: 30239679
Annu Rev Genet. 1984;18:1-29
pubmed: 6397121