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PlanMine specifications

Information


Unique identifier OMICS_10766
Name PlanMine
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Jochen C. Rink

Publications for PlanMine

PlanMine citations

 (13)
library_books

Identification of multiple isomeric core chitobiose–modified high mannose and paucimannose N glycans in the planarian Schmidtea mediterranea

2018
PMCID: 5936828
PMID: 29475940
DOI: 10.1074/jbc.RA117.000782

[…] gans (accession number NP_504545.2) and its avian homolog from C. livia (accession number FJ971845.1/ADC84389.1) were used as query sequences for a sequence similarity search using BLASTp against the PlanMine database (). All entries in the GT-92 glycosyltransferase family listed in the CAZy database () and the two putative GALT-1 sequences from S. mediterranea obtained from the sequence search we […]

library_books

A novel flatworm specific gene implicated in reproduction in Macrostomum lignano

2018
Sci Rep
PMCID: 5816591
PMID: 29453392
DOI: 10.1038/s41598-018-21107-4

[…] one and eight contigs identified in asexual (dd_Smed_v6) and sexual (dd_Smes_v1) transcriptome assemblies respectively (Supplementary Table ), as well as in all 5 other planarian species available in PlanMine. We did not find significant matches to the Mlig-SPERM1 protein in the transcriptomes of parasitic flatworms or outside flatworm species. Alignment of the representative proteins revealed a c […]

library_books

The abrogation of condensin function provides independent evidence for defining the self renewing population of pluripotent stem cells

2018
Dev Biol
PMCID: 5771471
PMID: 28757112
DOI: 10.1016/j.ydbio.2017.07.023

[…] , Homo sapiens and Mus musculus as queries. Condensins from other flatworm species (Schmidtea polychroa, Planaria torva, Dendrocoelum lacteum, Polycelis nigra and Polycelis tenuis) were obtained from Planmine (). Multiple sequence alignments of condensin proteins were performed using MAFFT () followed by phylogenetic tree generation using RAxML () using the gamma WAG model with 1000 bootstrap repl […]

call_split

Enzymatic degradation of organophosphorus insecticides decreases toxicity in planarians and enhances survival

2017
Sci Rep
PMCID: 5680213
PMID: 29123147
DOI: 10.1038/s41598-017-15209-8
call_split See protocol

[…] To identify a planarian homolog of Homo sapiens AChE (Hs-AChE) isoform E4-E5 precursor (NP_056646.1), we examined, via TBLASTN, the planarian transcriptome database PlanMine (http://planmine.mpi-cbg.de/planmine/begin.do) particularly the following flatworm species: S. mediterranea, P. torva, P. tenuis, D. lactum and S. polychroa. We identified sequences producing […]

call_split

A C terminally truncated form of β catenin acts as a novel regulator of Wnt/β catenin signaling in planarians

2017
PLoS Genet
PMCID: 5643146
PMID: 28976975
DOI: 10.1371/journal.pgen.1007030
call_split See protocol

[…] β-Catenin sequences from Planarian species were identified in the Planmine database []. β-Catenin sequences from Echinococcus multilocularis and Kronborgia cf. amphipodicola were found in the available databases [, ]. The rest of the sequences were found in the NCBI […]

call_split

Putrescine independent wound response phenotype is produced by ODC like RNAi in planarians

2017
Sci Rep
PMCID: 5574924
PMID: 28851936
DOI: 10.1038/s41598-017-09567-6
call_split See protocol

[…] me assembled from sequence reads obtained from wild-type D. japonica . S. mediterranea ODC homologous sequences, were obtained by searching the Schmidtea mediterranea genome database (SmedGD) and the Planmine database. Dugesia japonica homologs of Smed-NB22.11.e, Smed-agat-2, Smed-Collagen, were obtained by BLAST analysis using as input S. mediterranea nucleotide sequences. Blastn and tblastx sear […]

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PlanMine institution(s)
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
PlanMine funding source(s)
This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement number 649024) and the Max Planck Society.

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