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PLAZA 3.0 : an access point for plant comparative genomics

Sebastian Proost (UGent) , Michiel Van Bel (UGent) , Dries Vaneechoutte, Yves Van de Peer (UGent) , Dirk Inzé (UGent) , Bernd Mueller-Roeber and Klaas Vandepoele (UGent)
(2015) NUCLEIC ACIDS RESEARCH. 43(D1). p.D974-D981
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Abstract
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.
Keywords
ARABIDOPSIS, GENERATION, DATABASE, EVOLUTION, SEQUENCE, DRAFT GENOME, DATA SETS, RESOURCE, ALGORITHM, DUPLICATION

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MLA
Proost, Sebastian, et al. “PLAZA 3.0 : An Access Point for Plant Comparative Genomics.” NUCLEIC ACIDS RESEARCH, vol. 43, no. D1, 2015, pp. D974–81, doi:10.1093/nar/gku986.
APA
Proost, S., Van Bel, M., Vaneechoutte, D., Van de Peer, Y., Inzé, D., Mueller-Roeber, B., & Vandepoele, K. (2015). PLAZA 3.0 : an access point for plant comparative genomics. NUCLEIC ACIDS RESEARCH, 43(D1), D974–D981. https://doi.org/10.1093/nar/gku986
Chicago author-date
Proost, Sebastian, Michiel Van Bel, Dries Vaneechoutte, Yves Van de Peer, Dirk Inzé, Bernd Mueller-Roeber, and Klaas Vandepoele. 2015. “PLAZA 3.0 : An Access Point for Plant Comparative Genomics.” NUCLEIC ACIDS RESEARCH 43 (D1): D974–81. https://doi.org/10.1093/nar/gku986.
Chicago author-date (all authors)
Proost, Sebastian, Michiel Van Bel, Dries Vaneechoutte, Yves Van de Peer, Dirk Inzé, Bernd Mueller-Roeber, and Klaas Vandepoele. 2015. “PLAZA 3.0 : An Access Point for Plant Comparative Genomics.” NUCLEIC ACIDS RESEARCH 43 (D1): D974–D981. doi:10.1093/nar/gku986.
Vancouver
1.
Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, et al. PLAZA 3.0 : an access point for plant comparative genomics. NUCLEIC ACIDS RESEARCH. 2015;43(D1):D974–81.
IEEE
[1]
S. Proost et al., “PLAZA 3.0 : an access point for plant comparative genomics,” NUCLEIC ACIDS RESEARCH, vol. 43, no. D1, pp. D974–D981, 2015.
@article{5930884,
  abstract     = {{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.}},
  author       = {{Proost, Sebastian and Van Bel, Michiel and Vaneechoutte, Dries and Van de Peer, Yves and Inzé, Dirk and Mueller-Roeber, Bernd and Vandepoele, Klaas}},
  issn         = {{0305-1048}},
  journal      = {{NUCLEIC ACIDS RESEARCH}},
  keywords     = {{ARABIDOPSIS,GENERATION,DATABASE,EVOLUTION,SEQUENCE,DRAFT GENOME,DATA SETS,RESOURCE,ALGORITHM,DUPLICATION}},
  language     = {{eng}},
  number       = {{D1}},
  pages        = {{D974--D981}},
  title        = {{PLAZA 3.0 : an access point for plant comparative genomics}},
  url          = {{http://doi.org/10.1093/nar/gku986}},
  volume       = {{43}},
  year         = {{2015}},
}
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