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Protocols

PNRD specifications

Information


Unique identifier OMICS_06394
Name PNRD
Alternative name Plant Non-coding RNA Database
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Zhen Su

Publication for Plant Non-coding RNA Database

PNRD 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

[…] is a Wiki-based database of plant lncRNAs, in which lncRNAs from 37 plant species were annotated, whereas PLNlncRbase collects all experimentally-identified lncRNAs in 43 plant species. In addition, PNRD and CANTATAdb are the two largest plant lncRNAs databases. PNRD includes lncRNA sequences of mainly four plant species, including Arabidopsis, rice, poplar, and maize, while the recently-releas […]

library_books

Comparative analysis of miRNAs of two rapeseed genotypes in response to acetohydroxyacid synthase inhibiting herbicides by high throughput sequencing

2017
PLoS One
PMCID: 5614533
PMID: 28950015
DOI: 10.1371/journal.pone.0184917

[…] using bowtie and assigned the potential classification to these reads. Only the best-matched alignment was considered as the potential classification. The ta-siRNAs of 16 plants were downloaded from PNRD (Plant Non-coding RNA Database, http://structuralbiology.cau.edu.cn/PNRD/) []. The reads were then aligned with those ta-siRNAs to predict known conserved ta-siRNAs, according to a previous repor […]

library_books

Transcriptome analysis of Callery pear (Pyrus calleryana) reveals a comprehensive signalling network in response to Alternaria alternata

2017
PLoS One
PMCID: 5608294
PMID: 28934298
DOI: 10.1371/journal.pone.0184988

[…] entative characteristics of other species were identified as lncRNA candidates. A large number of predicted and validated plant lncRNAs can be searched in public databases, such as the NONCODE [] and PNRD [] databases. In addition, the CPC (Coding Potential Calculator), CNCI (Coding-Non-Coding Index), and PLEK (predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme) […]

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

[…] hairpin annotation” for miRNA prediction, and the ta-siRNA prediction tool. Besides, as noticed in Tables and , several valuable databases and bioinformatics tools, including Rice epigenome maps and PNRD, are currently terminated for unknown reason. We hope that these useful resources could be activated again for the plant biologists. Summarily, more research efforts, from both the bioinformatici […]

library_books

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

2017
BMC Genomics
PMCID: 5359931
PMID: 28320315
DOI: 10.1186/s12864-017-3623-8

[…] we conducted a BLAST search of all unique ‘primary’ transcripts against the SwissProt database (BLASTx, E-value = 1e-06) [], NCBI non-redundant (Nr) protein database (BLASTx, E-value = 1e-06) [], and Plant Non-coding RNA Database (BLASTn, E-value = 1e-06) []. Additionally, the ‘alternate’ transcripts sets were searched against the SwissProt database for annotation. For each sequence we retained th […]

call_split

Response of microRNAs to cold treatment in the young spikes of common wheat

2017
BMC Genomics
PMCID: 5330121
PMID: 28241738
DOI: 10.1186/s12864-017-3556-2
call_split See protocol

[…] tp://rfam.xfam.org/). The reads were identified as known miRNAs by the BLAST search against the miRBase 21 database with at most two mismatches (http://www.mirbase.org/), and the wheat microRNAs from PNRD (http://structuralbiology.cau.edu.cn/PNRD), PmiRExAt (http://pmirexat.nabi.res.in/), and IWGSC miRNA dataset [] with the perfect match. After the removal of the known small RNAs and repeat-associ […]


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PNRD institution(s)
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China

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