Plant snoRNA Database statistics

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Number of citations per year for the bioinformatics software tool Plant snoRNA Database
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Plant snoRNA Database specifications

Information


Unique identifier OMICS_03249
Name Plant snoRNA Database
Restrictions to use None
Version 1.2
Maintained Yes

Maintainer


  • person_outline Plant snoRNA Database

Publication for Plant snoRNA Database

Plant snoRNA Database citations

 (6)
library_books

Genome wide profiling of long non coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

2018
BMC Plant Biol
PMCID: 5935960
PMID: 29728060
DOI: 10.1186/s12870-018-1300-y

[…] h class code ‘o’ were kept; for intron lncRNAs, transcripts falling entirely within a reference intron were kept. Second, transcripts shorter than 200 bp were removed. Third, tomato EST database, the plant snoRNA database and the tomato sRNA database were used to filter the data set by BLASTN (EST filtering: E-value cutoff 1e-10, alignment coverage > 80%, and identity > 80%; housekeeping ncRNAs: E […]

library_books

Genome wide analysis of EgEVE_1, a transcriptionally active endogenous viral element associated to small RNAs in Eucalyptus genomes

2017
Genet Mol Biol
PMCID: 5452135
PMID: 28235127
DOI: 10.1590/1678-4685-GMB-2016-0086

[…] nse, Solanum lycopersicum and Vitis vinifera mitochondria (GenBank accessions AFYB00000000, NC_028254 and NC_012119), Populus tricocharpa and Vitis vinifera tRNAs from GtRNAdb () and snoRNAs from the Plant snoRNA database (http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home). Sequences that matched these references were discarded for further analysis. After this filtering, a total of 615,801 n […]

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Phylogenetic distribution of plant snoRNA families

2016
BMC Genomics
PMCID: 5122169
PMID: 27881081
DOI: 10.1186/s12864-016-3301-2

[…] preferrentially included species for which snoRNAs had been described in the literature.We collected all available plant snoRNA sequences from the SnoRNA orthologous gene database (SNOPY []) and the plant snoRNA database []. In addition we extracted snoRNA sequences from the literature [, , –].We considered only the rRNAs/snRNAs as potential targets. Ribosomal RNA sequences of the 24 plant and re […]

library_books

Identification of Reference Genes for Quantitative Expression Analysis of MicroRNAs and mRNAs in Barley under Various Stress Conditions

2015
PLoS One
PMCID: 4368757
PMID: 25793505
DOI: 10.1371/journal.pone.0118503

[…] gov/nuccore/X60343.1) and Hvu-ADP (AJ508228.2: http://www.ncbi.nlm.nih.gov/nuccore/AJ508228.2) were downloaded from the NCBI Genbank while the sequences of all barley snoRNAs were downloaded from the plant snoRNA database (http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home). The sequences of miR168 (accession number MIMAT0018216) and miR159 (accession number MIMAT0018210) were obtained from m […]

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Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars

2012
BMC Genomics
PMCID: 3527192
PMID: 23171001
DOI: 10.1186/1471-2164-13-657

[…] ntaining ambiguous nucleotides. From cleaned sequences, we further removed sRNAs aligned to the non-coding RNAs (ncRNA) such as rRNAs, tRNAs, snRNAs and snoRNAs. We collected ncRNAs from Rfam [], the Plant snoRNA Database [], and 19,350 rRNAs from the NCBI database. tRNAs were predicted with tRNAScan-SE [] for the strawberry reference genome. We predicted tRNAs from strawberry because it was used […]

library_books

ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure Based Dynamic Expression (DSDE) Analyses

2011
PMCID: 3037080
PMID: 21227933
DOI: 10.1093/pcp/pcq202

[…] s consisting of 39,361 TAIR9 gene models including alternative splicing variants and genes annotated as pseudogenes, 188 miRNA genes described in miRBase (Release 12) and 189 snoRNAs described in the plant snoRNA database (). A user can choose ARTADE2 gene models (DSDE) or annotated gene models (SSDE) and browse the list of all genes. Moreover, tables for annotated gene models with overlapping ART […]


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Plant snoRNA Database institution(s)
Gene Expression Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK

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