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Protocols

RNA STRAND specifications

Information


Unique identifier OMICS_03253
Name RNA STRAND
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline R STRAND Team

Additional information


http://www.rnasoft.ca/strand/help.php

Publication for RNA STRAND

RNA STRAND citations

 (55)
library_books

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model

2018
PLoS One
PMCID: 5886407
PMID: 29621250
DOI: 10.1371/journal.pone.0194583

[…] erformance of our algorithms, namely HK-PK, HK-PK-free, IP-pk168 and DK-pk16. HK-PK (with 88 pseudoknotted structures) and HK-PK-free (with 337 pseudoknot-free structures) datasets were compiled from RNA STRAND database and were used as test datasets in evaluating HotKnots V2.0 []; IP-pk168 (with 168 pseudoknotted structures) contains 16 categories of pseudoknotted structures with at most 85% sequ […]

library_books

Capturing the ‘ome’: the expanding molecular toolbox for RNA and DNA library construction

2018
Nucleic Acids Res
PMCID: 5888575
PMID: 29514322
DOI: 10.1093/nar/gky167

[…] the 5′ adaptor ligation step. This also reduces undesired products caused by excess unligated 3′ adaptor.Alternatively, the 5′ adaptor can be ligated to the first strand cDNA after degradation of the RNA strand, for instance through alkaline treatment () or RNase H digestion (Figure ). Provided that the 5′ adaptor (DNA) is 5′ adenylated and 3′ blocked, the ATP-independent thermostable Mth K97A (so […]

library_books

Chromatin associated RNA sequencing (ChAR seq) maps genome wide RNA to DNA contacts

2018
eLife
PMCID: 5962340
PMID: 29648534
DOI: 10.7554/eLife.27024.037

[…] to all dm3 transcriptomes from FlyBase (downloaded January 2016, versions r5.57): with the same bowtie2 parameters, but also first forcing sense strandedness as bridge orientation should preserve the RNA strand information, and then for reads that did not align in the sense direction, permitting antisense alignment. Reads that aligned with equal alignment score to more than one transcriptome were […]

library_books

Distinct fitness costs associated with the knockdown of RNAi pathway genes in western corn rootworm adults

2017
PLoS One
PMCID: 5739497
PMID: 29267401
DOI: 10.1371/journal.pone.0190208

[…] ys163) in the conserved motif (Tyr-Xaa3-Lys-Xaa(9–11)-Gln-Xaa(21–33)-Lys) of the PIWI domain that are believed to be involved in binding to the 5’ phosphate group of the first nucleotide of the guide RNA strand [] are all present in WCR Argonautes ().Also illustrated in , WCR Argonautes possess conserved metal chelating residues (Asp, Asp and His [DDH]) that are found in the catalytic motif of PIW […]

library_books

Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells

2017
Sci Rep
PMCID: 5550456
PMID: 28794451
DOI: 10.1038/s41598-017-08032-8

[…] vitamin B12 uptake is lower in S. Typhimurium than E. coli). Also, we have recently observed that conjugation of PNA with the (KFF)3K peptide hinders PNA hybridization efficiency with a complementary RNA strand. To determine if the attachment of vitamin B12 affects hybridization of a PNA oligomer with complementary RNA, we performed polyacrylamide gel electrophoresis (PAGE) experiments. We used th […]

library_books

Crystal structure of 2C helicase from enterovirus 71

2017
Sci Adv
PMCID: 5409451
PMID: 28508043
DOI: 10.1126/sciadv.1602573

[…] n the middle of the C-terminal helix (). The hexameric model of EV71 2C 116–329 suggests that the C-terminal RNA binding motif may be located on the rim of the ring structure. It is possible that one RNA strand simultaneously interacts with multiple RNA binding sites on the hexamer and plays an essential role in stabilizing the 2C hexamer. This hypothesis is supported by a biochemical and structur […]

Citations

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RNA STRAND institution(s)
Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
RNA STRAND funding source(s)
Supported by Mathematics of Information Technology and Complex Systems Network of Centres of Excellence and Natural Sciences and Engineering Research Council of Canada Discovery Grant Program (238788 and 217192).

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