PLAZA 3.0: an access point for plant comparative genomics
By S. Proost, Michiel Van Bel, Dries Vaneechoutte, Y. Van de Peer, Dirk Inzé, B. Mueller‐Roeber, K. Vandepoele. Nucleic Acids Res., 2014
324 citations recorded by the source corpus.
Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.
Subfields: Genetics, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/9829bdc1fb4a788458c5fceda237a44d2969ec7e
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Citations in the corpus
- The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, unknown): “Because orthologs are so important, a large number of methods and resources for their inference have been developed over the years, such as the COGs database (4), Inparanoid (5), OrthoMCL (6), En-sembl Compara (7), KEGG Orthology (8), PhylomeDb (9), OrthoDB (10), EggNOG (11), MBGD (12), PLAZA (13) o”
- PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics (2017, methodology): “Within the plant kingdom a variety of such platforms is available, each with a different focus, such as PLAZA (2), Phytozome (3), Gramene (4) and Ensembl Plants (5).”