RASP: an atlas of transcriptome-wide RNA secondary structure probing data.
Animals
COVID-19
/ epidemiology
Computational Biology
/ methods
Databases, Genetic
/ statistics & numerical data
Genome, Viral
/ genetics
High-Throughput Nucleotide Sequencing
/ methods
Humans
Nucleic Acid Conformation
Pandemics
RNA
/ chemistry
RNA Probes
/ genetics
RNA, Bacterial
/ chemistry
RNA, Fungal
/ chemistry
RNA, Plant
/ chemistry
RNA, Viral
/ chemistry
SARS-CoV-2
/ genetics
Transcriptome
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2021
08 01 2021
Historique:
accepted:
26
09
2020
revised:
13
09
2020
received:
14
08
2020
pubmed:
18
10
2020
medline:
26
1
2021
entrez:
17
10
2020
Statut:
ppublish
Résumé
RNA molecules fold into complex structures that are important across many biological processes. Recent technological developments have enabled transcriptome-wide probing of RNA secondary structure using nucleases and chemical modifiers. These approaches have been widely applied to capture RNA secondary structure in many studies, but gathering and presenting such data from very different technologies in a comprehensive and accessible way has been challenging. Existing RNA structure probing databases usually focus on low-throughput or very specific datasets. Here, we present a comprehensive RNA structure probing database called RASP (RNA Atlas of Structure Probing) by collecting 161 deduplicated transcriptome-wide RNA secondary structure probing datasets from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 experimental methods including DMS-seq, SHAPE-Seq, SHAPE-MaP, and icSHAPE, etc. Specially, RASP curates the up-to-date datasets of several RNA secondary structure probing studies for the RNA genome of SARS-CoV-2, the RNA virus that caused the on-going COVID-19 pandemic. RASP also provides a user-friendly interface to query, browse, and visualize RNA structure profiles, offering a shortcut to accessing RNA secondary structures grounded in experimental data. The database is freely available at http://rasp.zhanglab.net.
Identifiants
pubmed: 33068412
pii: 5929232
doi: 10.1093/nar/gkaa880
pmc: PMC7779053
doi:
Substances chimiques
RNA Probes
0
RNA, Bacterial
0
RNA, Fungal
0
RNA, Plant
0
RNA, Viral
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D183-D191Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
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