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Protocols

PomBase specifications

Information


Unique identifier OMICS_06183
Name PomBase
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/PomBase

Taxon


  • Plants and Fungi
    • Schizosaccharomyces pombe

Maintainer


  • person_outline Mark D. McDowall

Publications for PomBase

PomBase citations

 (45)
library_books

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

2018
PMCID: 5872342
DOI: 10.3390/jof4010039

[…] ata (user comments, see below).The Link outs section offers redirection to other resources including EnsemblFungi [], Entrez Gene [], FGSC [], UniProt [], JGI [], PHI-Base [], AspGD [], PhylomeDB [], PomBase [], CGD [], SGD [], and others.The Genomic Location section contains gene or sequence coordinates within a chromosome or contig/scaffold and a link out to GBrowse.The Literature section provid […]

library_books

Non B Form DNA Is Enriched at Centromeres

2018
Mol Biol Evol
PMCID: 5889037
PMID: 29365169
DOI: 10.1093/molbev/msy010

[…] monkey, the RefSeq Chlorocebus sabaeus assembly (accession GCF_000409795.2) was hard-masked using RepeatMasker annotations available from RefSeq. The S. pombe assembly (ASM294v2) was downloaded from PomBase (); the S. mikatae (IFO 1815T) and S. kudriavzevii (IFO 1815T) ultra-scaffolds were previously published () and are available online (http://sss.genetics.wisc.edu/cgi-bin/s3.cgi; last accessed […]

library_books

Genes Important for Schizosaccharomyces pombe Meiosis Identified Through a Functional Genomics Screen

2017
Genetics
PMCID: 5788524
PMID: 29259000
DOI: 10.1534/genetics.117.300527

[…] between 2 and 7 were selected for MS2. The MaxQuant software platform () version 1.5.2.8 was used to process the raw files and search was conducted against S. pombe complete/reference proteome set of PomBase database (released on 01/07/2016), using the Andromeda search engine (). For the first search peptide tolerance was set to 20 ppm while for the main search peptide tolerance was set to 4.5 ppm […]

call_split

Phosphorylation of the RNA binding protein Zfs1 modulates sexual differentiation in fission yeast

2017
PMCID: 5769579
PMID: 29084823
DOI: 10.1242/jcs.208066
call_split See protocol

[…] ogy. Ribosomal RNA was depleted from samples by using the Illumina Ribo-Zero Gold rRNA removal kit. All sequences were initially mapped to the S. pombe genome sequence, downloaded on 16 Sep 2013 from PomBase (www.pombase.org). A reference transcriptome was reconstructed by using RSEM (version 1.1.19) () from an annotation file in GTF format downloaded from PomBase. Subsequent mapping and read coun […]

library_books

Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data

2017
Nucleic Acids Res
PMCID: 5753374
PMID: 29155944
DOI: 10.1093/nar/gkx1116

[…] ition, protein and/or GI data are also available through species-specific databases such as DroID () and FlyBase () for Drosophila, Human Protein Reference Database (HPRD) for human and mouse (), and PomBase () for fission yeast.A challenge for bench scientists who are interested to mine and use protein or GI data is that these various resources have different coverage and the results obtained for […]

library_books

The Schizosaccharomyces pombe PPR protein Ppr10 associates with a novel protein Mpa1 and acts as a mitochondrial translational activator

2017
Nucleic Acids Res
PMCID: 5389468
PMID: 28334955
DOI: 10.1093/nar/gkx127

[…] ral role in mt-RNA expression; however, the data have not been published (). This protein has a molecular size of 59 kDa (515 amino acids) and is classified as orphan in the S. pombe genome database, PomBase (http://www.pombase.org/). A standard BLAST search, with Ppr10 as the query, revealed that close homologs of Ppr10 exist only in other recently sequenced fission yeast species, Schizosaccharom […]

Citations

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PomBase institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK; Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Cambridge, Cambridgeshire, UK; Research Department of Genetics, Evolution and Environment, and UCL Cancer Institute, University College London, Darwin Building, London, UK

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