PeroxisomeDB statistics

Tool stats & trends

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Protocols

PeroxisomeDB specifications

Information


Unique identifier OMICS_02762
Name PeroxisomeDB
Alternative names Peroxisome DataBase, PeroxisomeDB 2.0
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens

Subtools


  • Organelle Predictor
  • PTSs Predictor

Maintainers


  • person_outline Aurora Pujol
  • person_outline Agatha Schlüter

Publications for Peroxisome DataBase

PeroxisomeDB citations

 (5)
library_books

A eukaryotic nicotinate inducible gene cluster: convergent evolution in fungi and bacteria

2017
Open Biol
PMCID: 5746545
PMID: 29212709
DOI: 10.1098/rsob.170199

[…] with Figtree (http://tree.bio.ed.ac.uk/software/figtree/, http://mafft.cbrc.jp/alignment/server/) and localization signals were searched for at http://www.cbs.dtu.dk/services/TargetP/ [], http://www.peroxisomedb.org/ [], http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi [], http://wolfpsort.org/ [], http://genome.unmc.edu/ngLOC/cite.html []. Structural analysis and modelling was carrie […]

library_books

Distribution and Evolution of Peroxisomes in Alveolates (Apicomplexa, Dinoflagellates, Ciliates)

2017
Genome Biol Evol
PMCID: 5755239
PMID: 29202176
DOI: 10.1093/gbe/evx250

[…] erentiate between orthologs and paralogs.Peroxisomal proteins for BLAST analyses were retrieved from the “peroxisome pathway” of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database () and the PeroxisomeDB (). Proteins of the ciliate T. thermophila were preferentially used as query sequences for local and online BLAST searches in our newly established transcriptomes and the alveolate refere […]

library_books

Predicting the targeting of tail anchored proteins to subcellular compartments in mammalian cells

2017
PMCID: 5450235
PMID: 28325759
DOI: 10.1242/jcs.200204

[…] s were created with GraphPad Prism 5 (GraphPad Software) with whiskers representing the smallest and largest value in the sample. PEX19-binding sites were analyzed using the BLOCKS algorithm from the PeroxisomeDB 2.0 database ().For the support vector machine (SVM) classifier (), we trained a SVM classifier with the [protein data] using the SVM application in package e1071 (), of the R statistical […]

call_split

Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals

2014
PLoS Genet
PMCID: 4207609
PMID: 25340584
DOI: 10.1371/journal.pgen.1004685
call_split See protocol

[…] g the following regular expression:(∧\*[∧*]*?([ASTPCE]RL|[SATPCVNG]KL|S[SNH]L|ARI|S[KR]M|[AG]NL|SN[IM]|[SA][KRQ]Y|HHL|[QS][KRQ]F)\*). PTS2 motifs were predicted with TargetSignalPredictor (http://www.peroxisomedb.org). Data analysis was performed with NCBI (National Center for Biotechnology Information) Basic local alignment search tool (Blast) , other NCBI resources and GenRE - MIPS Ustilago mayd […]

library_books

Targeting a heterologous protein to multiple plant organelles via rationally designed 5′ mRNA tags

2013
J Biol Eng
PMCID: 3847293
PMID: 24011257
DOI: 10.1186/1754-1611-7-20

[…] -2 sequences were predicted using the NetPlantGene server []. Targeting to the chloroplast and peroxisome of the TriTag-1 and TriTag-2 splice variants and TriTag-3 were predicted using TargetP [] and PeroxisomeDB 2.0 []. Peptide structures of CTPb and TriTag-3 were determined using PROFbval on the ROSTLAB server []. […]

Citations

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PeroxisomeDB institution(s)
Centre de Genetica Medica i Molecular, Institut d’Investigacio Biomedica de Bellvitge-Institut de Recerca Oncologica (IDIBELL-IRO), Hospital Duran i Reynals, Hospitalet de Llobregat, Barcelona, Spain; Bioinformatics Department, Centro de Investigacion Prıncipe Felipe, Spain; Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP/Collège de, France, Illkirch, France; Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Department of Pediatrics, Emma Children’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
PeroxisomeDB funding source(s)
Supported by funds from the Institut National de la Santé et de la Recherche Médicale, the Centre National de la Recherche Scientifique, the European Commission contract n° LSHM-CT2004-502987, the Association Française contre les Myopathies (Project n° 9315) the European Leukodystrophy Association and the Asociacion Espanola contra la Leucodistrofia (ALE-ELA Espana) and a recipient of FIS (CA05/0090) from the Instituto de Salud Carlos III.

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