PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

被引：92
|
作者：
Van Bel, Michiel [1 ,2 ]
Silvestri, Francesca [1 ,2 ]
Weitz, Eric M. [3 ]
Kreft, Lukasz [4 ]
Botzki, Alexander [5 ]
Coppens, Frederik [1 ,2 ]
Vandepoele, Klaas [1 ,2 ,6 ]
机构：
[1] Univ Ghent, Dept Plant Biotechnol & Bioinformat, Technol Pk 71, B-9052 Ghent, Belgium
[2] VIB Ctr Plant Syst Biol, Technol Pk 71, B-9052 Ghent, Belgium
[3] Broad Inst MIT & Harvard, Data Sci Platform, Cambridge, MA 02142 USA
[4] Polish Acad Sci, Inst Biochem & Biophys, Pawinskiego 5A, PL-02106 Warsaw, Poland
[5] VIB Bioinformat Core, B-9052 Ghent, Belgium
[6] Univ Ghent, Bioinformat Inst Ghent, Technol Pk 71, B-9052 Ghent, Belgium
来源：
NUCLEIC ACIDS RESEARCH | 2022年 / 50卷 / D1期
关键词：
GENE;
D O I：
10.1093/nar/gkab1024
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a broad set of genomes, data types and analysis tools available to researchers through a user-friendly website, an API, and bulk downloads. In this latest release of the PLAZA platform, we are integrating a record number of 134 high-quality plant genomes, split up over two instances: PLAZA Dicots 5.0 and PLAZA Monocots 5.0. This number of genomes corresponds with a massive expansion in the number of available species when compared to PLAZA 4.0, which offered access to 71 species, a 89% overall increase. The PLAZA 5.0 release contains information for 5 882 730 genes, and offers pre-computed gene families and phylogenetic trees for 5 274 684 protein-coding genes. This latest release also comes with a set of new and updated features: a new BED import functionality for the workbench, improved interactive visualizations for functional enrichments and genome-wide mapping of gene sets, and a fully redesigned and extended API. Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics. All PLAZA releases are accessible from the portal website: https://bioinformatics.psb.ugent.be/plaza/.
引用
收藏
页码：D1468 / D1474
页数：7
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