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PLAZA 3.0: an access point for plant comparative genomics.

Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, Vandepoele K - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.

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Gene page in PLAZA 3.0. From top to bottom, (A) the header with the menu and search functions, (B) the general information (links to the gene family, alternative gene names or identifiers) and Descriptions for gene AT1G01720, (C) the toolbox that allows different actions to be performed, (D) tabs with detailed functional information and (E) the footer with links to general information. A similar layout is consistently used on all pages describing different data types.
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Figure 1: Gene page in PLAZA 3.0. From top to bottom, (A) the header with the menu and search functions, (B) the general information (links to the gene family, alternative gene names or identifiers) and Descriptions for gene AT1G01720, (C) the toolbox that allows different actions to be performed, (D) tabs with detailed functional information and (E) the footer with links to general information. A similar layout is consistently used on all pages describing different data types.

Mentions: On the PLAZA portal each data type has its own page, with an intuitive and consistent layout. The top of the page highlights the most general information, with more specific and detailed information further down the page. Numerous hyperlinks are present to allow users to go from one type of data to another (e.g. from a gene to its family or orthologs, or from a gene family to a phylogenetic tree). Every page also has its own toolbox, which provides links to additional analyses and detailed visualizations (Figure 1).


PLAZA 3.0: an access point for plant comparative genomics.

Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, Vandepoele K - Nucleic Acids Res. (2014)

Gene page in PLAZA 3.0. From top to bottom, (A) the header with the menu and search functions, (B) the general information (links to the gene family, alternative gene names or identifiers) and Descriptions for gene AT1G01720, (C) the toolbox that allows different actions to be performed, (D) tabs with detailed functional information and (E) the footer with links to general information. A similar layout is consistently used on all pages describing different data types.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384038&req=5

Figure 1: Gene page in PLAZA 3.0. From top to bottom, (A) the header with the menu and search functions, (B) the general information (links to the gene family, alternative gene names or identifiers) and Descriptions for gene AT1G01720, (C) the toolbox that allows different actions to be performed, (D) tabs with detailed functional information and (E) the footer with links to general information. A similar layout is consistently used on all pages describing different data types.
Mentions: On the PLAZA portal each data type has its own page, with an intuitive and consistent layout. The top of the page highlights the most general information, with more specific and detailed information further down the page. Numerous hyperlinks are present to allow users to go from one type of data to another (e.g. from a gene to its family or orthologs, or from a gene family to a phylogenetic tree). Every page also has its own toolbox, which provides links to additional analyses and detailed visualizations (Figure 1).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.

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