Visualization of the small RNA transcriptome using seqclusterViz.
miRNA
report
sequencing
small RNA
snoRNA
tRNA
visualization
Journal
F1000Research
ISSN: 2046-1402
Titre abrégé: F1000Res
Pays: England
ID NLM: 101594320
Informations de publication
Date de publication:
Historique:
accepted:
20
02
2019
entrez:
16
4
2019
pubmed:
16
4
2019
medline:
16
4
2019
Statut:
epublish
Résumé
The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson's disease .
Identifiants
pubmed: 30984380
doi: 10.12688/f1000research.18142.1
pmc: PMC6446497
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Déclaration de conflit d'intérêts
No competing interests were disclosed.
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