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RoboOligo specifications

Information


Unique identifier OMICS_08083
Name RoboOligo
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

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Publication for RoboOligo

RoboOligo citations

 (4)
library_books

Mapping Post Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry

2017
Biomolecules
PMCID: 5372733
PMID: 28241457
DOI: 10.3390/biom7010021

[…] t user-friendly tool for ab initio oligonucleotide sequencing, it did not automate the process of data annotation. Additional tools soon followed, including RNA Mass Mapping (RRM) [], Ariadne [], and RoboOligo [].RRM was developed primarily for MALDI-MS data to enable RNA identification by matching RNase T1 digestion products to those predicted from RNA sequences available in a database. Ariadne u […]

library_books

tRNA mediated codon biased translation in mycobacterial hypoxic persistence

2016
Nat Commun
PMCID: 5114619
PMID: 27834374
DOI: 10.1038/ncomms13302

[…] h matching the retention times for their predicted c1 and y1 transitions were sequenced by targeted MS2 on the LC-QTOF at collision energies of 0, 15, 30 and 45 V. Fragment analysis, aided by SOS and RoboOligo, enabled us to map the exact location of each modification based on their a-B, c, w and y ions. The analysis of free bases and internal fragments (mainly matching ion fragments with w type c […]

library_books

Enhanced Detection of Post Transcriptional Modifications Using a Mass Exclusion List Strategy for RNA Modification Mapping by LC MS/MS

2015
Anal Chem
PMCID: 4542202
PMID: 26176336
DOI: 10.1021/acs.analchem.5b01826

[…] equences or the known post-transcriptionally modified E. coli tRNA sequences using the MongoOligo calculator (http://mods.rna.albany.edu/masspec/Mongo-Oligo). Automated annotation was conducted using RoboOligo and in-house software. The criterion for detection of a particular RNase T1 digestion product based on MS/MS analysis was at least 80% of the expected c- and y-type ions were found during sp […]

library_books

The identification and characterization of non coding and coding RNAs and their modified nucleosides by mass spectrometry

2015
RNA Biol
PMCID: 4615682
PMID: 25616408
DOI: 10.4161/15476286.2014.992280

[…] d OPA, which allow analysis of MS and MS/MS data with a customizable database of nucleotides, thus all known RNA modifications can be analyzed. Most recently, we have reported on the software program RoboOligo (http://bearcatms.uc.edu/new/limbachgroup_publication/robooligo-software.html), which allows for the manual annotation of MS/MS data from modified oligonucleotides. Further, RoboOligo also h […]


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RoboOligo institution(s)
Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
RoboOligo funding source(s)
National Institutes of Health [GM058843 to P.A.L., GM084065-07 to J.D.A.]

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