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Protocols

pico-PLAZA specifications

Information


Unique identifier OMICS_03163
Name pico-PLAZA
Restrictions to use None
Maintained Yes

Publication for pico-PLAZA

pico-PLAZA citations

 (6)
library_books

Conservation of Nonsense Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution

2017
Sci Rep
PMCID: 5709506
PMID: 29192227
DOI: 10.1038/s41598-017-16942-w

[…] e 24), 55 metazoan genomes from Ensembl Metazoa (release 24), and 37 protista genomes from Ensembl Protists (release 24). For green plants and algae, we used the 51 species available in PLAZA 3.0 and pico PLAZA. The proteins for the basal fungal lineages (i.e. in total 42 species from Cryptomycota, Microsporidia, Neocallimastigomycota, Chytridiomycota, Blastocladiomycota, Kickxellomycotina, Entomo […]

library_books

Population genomics of picophytoplankton unveils novel chromosome hypervariability

2017
Sci Adv
PMCID: 5498103
PMID: 28695208
DOI: 10.1126/sciadv.1700239

[…] with genes from the annotation of RCC4221 and RCC1115. Orthologous gene families of five gene sequences of predicted housekeeping genes trapped in the MAT locus region of O. tauri were retrieved from pico-PLAZA (), and genes that were located in the low-GC region of the big outlier chromosomes in all seven sequenced Mamiellophyceae species (O. tauri, O. lucimarinus, Micromonas RCC299 and CCMP1545, […]

library_books

Genome Wide Survey and Expression Analysis of Chlamydomonas reinhardtii U box E3 Ubiquitin Ligases (CrPUBs) Reveal a Functional Lipid Metabolism Module

2015
PLoS One
PMCID: 4378952
PMID: 25822994
DOI: 10.1371/journal.pone.0122600

[…] he bottom on C. reinhardtii chromosomes according to their positions. The homologous chromosome segments were detected using a synteny plot in Plaza (http://bioinformatics.psb.ugent.be/plaza/versions/pico-plaza/synteny/index). The CrPUB genes were subjected to BLAST analysis in Plaza, and their duplication patterns were detected using a synteny plot. […]

call_split

Functional characterization of the diatom cyclin dependent kinase A2 as a mitotic regulator reveals plant like properties in a non green lineage

2015
BMC Plant Biol
PMCID: 4392632
PMID: 25887918
DOI: 10.1186/s12870-015-0469-6
call_split See protocol

[…] (A. thaliana, C. merolae, C. reinhardtii, D. melanogaster, H. sapiens, N. gaditana, P. sojae, S. cerevisiae, S. pombe and X. laevis), through the JGI portal (P. tricornutum and T. pseuodonana) or the pico-PLAZA database (E. siliculosus, F. cylindrus, M. pusilla, M. sp., O. tauri and O. lucimarinus) [,]. Multiple alignments based on CDK amino acid sequences were generated with MUSCLE [] and then ma […]

library_books

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

2014
BMC Genomics
PMCID: 4378021
PMID: 25494611
DOI: 10.1186/1471-2164-15-1103

[…] amilies (number and presence of homologous genes) within sequenced green alga and land plants genomes, corresponding to the genes containing non-sense or frameshift mutations, were retrieved from the pico-PLAZA database []. The absence of a homologous gene was further confirmed by a tblastn against the genome sequence.To investigate copy number variations between 2001 and 2009, we analysed the cov […]

library_books

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

2012
Genome Biol
PMCID: 3491373
PMID: 22925495
DOI: 10.1186/gb-2012-13-8-r74

[…] .0 was used (Additional file ) [] and all chromosomes from all species were compared against each other and significant colinear regions were identified. All gene colinearity can be browsed using the pico-PLAZA comparative genomics platform []. i-ADHoRe was run with the following settings: alignment_method gg, gap_size 30, cluster_gap 35, q_value 0.9, prob_cutoff 0.0001, anchor_points 5 and level_ […]

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pico-PLAZA institution(s)
Department of Plant Systems Biology, VIB, Gent, Belgium

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