PLncDB statistics

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Protocols

PLncDB specifications

Information


Unique identifier OMICS_09889
Name PLncDB
Alternative name Plant long non-coding RNA database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


This tool is not available anymore.

Publication for Plant long non-coding RNA database

PLncDB citations

 (7)
library_books

Non coding RNAs and Their Roles in Stress Response in Plants

2017
PMCID: 5673675
PMID: 29017967
DOI: 10.1016/j.gpb.2017.01.007

[…] d lncRNAdb, there are several plant-specific lncRNA databases available. Through integrating multi-omics datasets, such as tilling array, RNA-seq, epigenetic, and small RNA data, Jin et al. developed PlncDB, which provides comprehensive information related to lncRNAs, but only for Arabidopsis . GREENC is a Wiki-based database of plant lncRNAs, in which lncRNAs from 37 plant species were annotated […]

library_books

Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

2017
PMCID: 5545994
PMID: 28786034
DOI: 10.1186/s12284-017-0177-y

[…] uge sRNA sequencing (sRNA-seq) datasets onto a plant genome, Bowtie should be selected as one of the powerful tools (Langmead et al., ). miRBase (the microRNA database) (Griffiths-Jones et al., ) and PLncDB (plant long non-coding RNA database) (Jin et al., ) are useful to check whether the sRNA is originated from a miRNA precursor or a lncRNA. Besides, ShortStack should be a useful tool to analyze […]

library_books

Long non coding RNA Databases in Cardiovascular Research

2016
PMCID: 4996844
PMID: 27049585
DOI: 10.1016/j.gpb.2016.03.001

[…] NAMap . Many of these databases provide information for human and murines only, but there are also databases specialized in other model organisms such as zflncRNApedia for zebrafish (Danio rerio) or PLncDB for Arabidopsis thaliana. […]

call_split

Genome Wide Identification and Characterization of Long Non Coding RNAs from Mulberry (Morus notabilis) RNA seq Data

2016
Genes
PMCID: 4808792
PMID: 26938562
DOI: 10.3390/genes7030011
call_split See protocol

[…] To further demonstrate the reliability of lncRNAs predicted from the RNA-seq data and calculate the conservation of the novel lncRNAs, a set of lncRNAs collected by TAIR [] and PlncDB [] was downloaded and then aligned with the sequences of novel mulberry lncRNAs using BLASTN software []. […]

library_books

Promoter based identification of novel non coding RNAs reveals the presence of dicistronic snoRNA miRNA genes in Arabidopsis thaliana

2015
BMC Genomics
PMCID: 4660826
PMID: 26607788
DOI: 10.1186/s12864-015-2221-x

[…] otations. For that purpose, we used annotations contained in the Arabidopsis TAIR10 database [] and information contained in both the microRNA database (miRBase) [] and the Plant Long ncRNA database (PLncDB) []. Finally, all predicted ncRNA candidates passing the above criteria were analyzed using Rfam, which reported the full collection of validated ncRNAs and their classification into distinct R […]

library_books

Transcriptome wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

2015
BMC Genomics
PMCID: 4647491
PMID: 26572793
DOI: 10.1186/s12864-015-2108-x

[…] ed 35,000 Arabidopsis transcripts and 50,000 soybean coding transcripts. The negative training set included non-redundant known Arabidopsis noncoding transcripts from 3 resources: (i) 25,000 from the plant long non-coding RNA database PLncDB [], (ii) 3,800 from the NONCODE version 4 database [], and (iii) 278 from TAIR10 []. There is currently no available source for noncoding soybean transcripts. […]

Citations

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PLncDB institution(s)
Laboratory of Plant Molecular Biology, Chinakefeller University, New York, NY, USA; School of Computing, National University of Singapore, Singapore

PLncDB reviews

 (2)
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Mavis Lee

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Dataset
DEAD

Sangram keshari sahu

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Dataset
This site is no more reachable. I have tried several time in the past, contacted the author also. Doesn't seems like resolved yet.