PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

被引：202

作者：

Proost, Sebastian ^{[1
,2
]}

Van Bel, Michiel ^{[1
,2
]}

Sterck, Lieven ^{[1
,2
]}

Billiau, Kenny ^{[1
,2
]}

Van Parys, Thomas ^{[1
,2
]}

Van de Peer, Yves ^{[1
,2
]}

Vandepoele, Klaas ^{[1
,2
]}

机构：

[1] Flanders Inst Biotechnol, Dept Plant Syst Biol, B-9052 Ghent, Belgium

[2] Univ Ghent, Dept Mol Genet, B-9052 Ghent, Belgium

来源：

PLANT CELL | 2009年 / 21卷 / 12期

关键词：

REGULATORY ELEMENTS; HISTONE GENES; WHOLE-GENOME; ARABIDOPSIS; SEQUENCE; PLATFORM; DATABASE; RECONCILIATION; IDENTIFICATION; ANNOTATION;

D O I：

10.1105/tpc.109.071506

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：

The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.

引用

页码：3718 / 3731

页数：14

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