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pico-PLAZA, a genome database of microbial photosynthetic eukaryotes

(2013) ENVIRONMENTAL MICROBIOLOGY. 15(8). p.2147-2153
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. PLAZA can be used to functionally characterize large-scale ES /RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylumtricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.
Keywords
FEATURES, HISTORY, UNIQUE, SEQUENCE, PICOPLANKTON, ECOLOGY, REVEALS, EVOLUTION, GENETIC DIVERSITY, DIATOM GENOMES

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Citation

Please use this url to cite or link to this publication:

Chicago
Vandepoele, Klaas, Michiel Van Bel, Guilhem Richard, Sofie Van Landeghem, Bram Verhelst, Hervé Moreau, Yves Van de Peer, Nigel Grimsley, and Gwenael Piganeau. 2013. “pico-PLAZA, a Genome Database of Microbial Photosynthetic Eukaryotes.” Environmental Microbiology 15 (8): 2147–2153.
APA
Vandepoele, Klaas, Van Bel, M., Richard, G., Van Landeghem, S., Verhelst, B., Moreau, H., Van de Peer, Y., et al. (2013). pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. ENVIRONMENTAL MICROBIOLOGY, 15(8), 2147–2153.
Vancouver
1.
Vandepoele K, Van Bel M, Richard G, Van Landeghem S, Verhelst B, Moreau H, et al. pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. ENVIRONMENTAL MICROBIOLOGY. 2013;15(8):2147–53.
MLA
Vandepoele, Klaas, Michiel Van Bel, Guilhem Richard, et al. “pico-PLAZA, a Genome Database of Microbial Photosynthetic Eukaryotes.” ENVIRONMENTAL MICROBIOLOGY 15.8 (2013): 2147–2153. Print.
@article{4127420,
  abstract     = {With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. PLAZA can be used to functionally characterize large-scale ES /RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylumtricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.},
  author       = {Vandepoele, Klaas and Van Bel, Michiel and Richard, Guilhem and Van Landeghem, Sofie and Verhelst, Bram and Moreau, Herv{\'e} and Van de Peer, Yves and Grimsley, Nigel and Piganeau, Gwenael},
  issn         = {1462-2912},
  journal      = {ENVIRONMENTAL MICROBIOLOGY},
  keyword      = {FEATURES,HISTORY,UNIQUE,SEQUENCE,PICOPLANKTON,ECOLOGY,REVEALS,EVOLUTION,GENETIC DIVERSITY,DIATOM GENOMES},
  language     = {eng},
  number       = {8},
  pages        = {2147--2153},
  title        = {pico-PLAZA, a genome database of microbial photosynthetic eukaryotes},
  url          = {http://dx.doi.org/10.1111/1462-2920.12174},
  volume       = {15},
  year         = {2013},
}

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