PMID- 27821510
OWN - NLM
STAT- MEDLINE
DCOM- 20170907
LR  - 20240324
IS  - 1469-9001 (Electronic)
IS  - 1355-8382 (Print)
IS  - 1355-8382 (Linking)
VI  - 23
IP  - 2
DP  - 2017 Feb
TI  - RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid 
      probing.
PG  - 240-249
LID - 10.1261/rna.058404.116 [doi]
AB  - Chemical and enzymatic probing of RNA secondary structure and RNA/protein 
      interactions provides the basis for understanding the functions of structured 
      RNAs. However, the ability to rapidly perform such experiments using capillary 
      electrophoresis has been hampered by relatively labor-intensive data analysis 
      software. While these computationally robust programs have been shown to 
      calculate residue-specific reactivities to a high degree of accuracy, they often 
      require time-consuming manual intervention and lack the ability to be easily 
      modified by users. To alleviate these issues, RiboCAT (Ribonucleic acid 
      capillary-electrophoresis analysis tool) was developed as a user-friendly, 
      Microsoft Excel-based tool that reduces the need for manual intervention, thereby 
      significantly shortening the time required for data analysis. Features of this 
      tool include (i) the use of an Excel platform, (ii) a method of intercapillary 
      signal alignment using internal size standards, (iii) a peak-sharpening algorithm 
      to more accurately identify peaks, and (iv) an open architecture allowing for 
      simple user intervention. Furthermore, a complementary tool, RiboDOG (RiboCAT 
      data output generator) was designed to facilitate the comparison of multiple data 
      sets, highlighting potential inconsistencies and inaccuracies that may have 
      occurred during analysis. Using these new tools, the secondary structure of the 
      HIV-1 5' untranslated region (5'UTR) was determined using selective 2'-hydroxyl 
      acylation analyzed by primer extension (SHAPE), matching the results of previous 
      work.
CI  - (c) 2017 Cantara et al.; Published by Cold Spring Harbor Laboratory Press for the 
      RNA Society.
FAU - Cantara, William A
AU  - Cantara WA
AD  - Department of Chemistry and Biochemistry, Center for Retrovirus Research, and 
      Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA.
FAU - Hatterschide, Joshua
AU  - Hatterschide J
AD  - Department of Chemistry and Biochemistry, Center for Retrovirus Research, and 
      Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA.
FAU - Wu, Weixin
AU  - Wu W
AD  - Department of Chemistry and Biochemistry, Center for Retrovirus Research, and 
      Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA.
FAU - Musier-Forsyth, Karin
AU  - Musier-Forsyth K
AD  - Department of Chemistry and Biochemistry, Center for Retrovirus Research, and 
      Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA.
LA  - eng
GR  - P50 GM103368/GM/NIGMS NIH HHS/United States
GR  - R01 GM065056/GM/NIGMS NIH HHS/United States
GR  - R01 GM113887/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20161107
PL  - United States
TA  - RNA
JT  - RNA (New York, N.Y.)
JID - 9509184
RN  - 0 (5' Untranslated Regions)
RN  - 0 (Nucleic Acid Probes)
RN  - 0 (RNA, Viral)
SB  - IM
MH  - 5' Untranslated Regions
MH  - Acylation
MH  - *Algorithms
MH  - Base Pairing
MH  - Base Sequence
MH  - Electrophoresis, Capillary/*statistics & numerical data
MH  - HIV-1/chemistry/genetics
MH  - Nucleic Acid Conformation
MH  - Nucleic Acid Probes/*analysis/chemistry
MH  - RNA, Viral/*analysis/chemistry
MH  - *Software
PMC - PMC5238798
OTO - NOTNLM
OT  - RNA structure
OT  - SHAPE
OT  - capillary electrophoresis
OT  - secondary structure
EDAT- 2016/11/09 06:00
MHDA- 2017/09/08 06:00
PMCR- 2018/02/01
CRDT- 2016/11/09 06:00
PHST- 2016/07/27 00:00 [received]
PHST- 2016/11/02 00:00 [accepted]
PHST- 2016/11/09 06:00 [pubmed]
PHST- 2017/09/08 06:00 [medline]
PHST- 2016/11/09 06:00 [entrez]
PHST- 2018/02/01 00:00 [pmc-release]
AID - rna.058404.116 [pii]
AID - RA [pii]
AID - 10.1261/rna.058404.116 [doi]
PST - ppublish
SO  - RNA. 2017 Feb;23(2):240-249. doi: 10.1261/rna.058404.116. Epub 2016 Nov 7.