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HiTRACE specifications

Information


Unique identifier OMICS_23828
Name HiTRACE
Alternative names High-Throughput Robust Analysis for Capillary Electrophoresis, HiTRACE-Web
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

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Additional information


http://hitrace.org/index.php/page/view/about

Publications for High-Throughput Robust Analysis for Capillary Electrophoresis

HiTRACE citations

 (12)
library_books

Hidden Structural Modules in a Cooperative RNA Folding Transition

2018
Cell Rep
PMCID: 5894117
PMID: 29562180
DOI: 10.1016/j.celrep.2018.02.101

[…] Footprinting data in the form of electrophoretic traces were aligned and processed using the established HiTRACE pipeline (; ). Peaks were quantified by fitting to a sum of Gaussian distributions. Relative uncertainties were generated from the sum of the squares of SDs upon shifting all peak positions by […]

library_books

Mechanism and structural diversity of exoribonuclease resistant RNA structures in flaviviral RNAs

2018
Nat Commun
PMCID: 5760640
PMID: 29317714
DOI: 10.1038/s41467-017-02604-y

[…] 3500 XL Genetic Analyzer. All reactions were performed in triplicate, as were “no modification” control reactions and ddNTP ladders. Analysis of capillary electrophoresis data was performed using the HiTRACE MATLAB toolkit (MathWorks) and 1D analysis pipeline developed by the Das and Yoon labs–. For further information, the website and tutorial for these programs and protocols can be found at: htt […]

library_books

Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four dimensional chemical mapping

2018
eLife
PMCID: 5847336
PMID: 29446752
DOI: 10.7554/eLife.29602.097

[…] The HiTRACE 2.0 software was used to analyze CE (capillary electrophoresis) data (; ; ). Electrophoretic traces were aligned and baseline subtracted using linear and non-linear alignment routines as previ […]

library_books

In Vivo Characterization of an AHR Dependent Long Noncoding RNA Required for Proper Sox9b Expression

2017
PMCID: 5438132
PMID: 28385905
DOI: 10.1124/mol.117.108233

[…] hods are summarized in . Wild-type RNA reference ladders were created using 3′dideoxy-TTP in an equilmolar amount to dTTP during the reverse transcription reaction. The SHAPE data were analyzed using HiTRACE-WEB (). Replicates from three independent samples were compared, and we performed a signal decay correction step to normalize for the typical exponential decay in fluorescent intensity as a fu […]

library_books

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch

2016
Nat Commun
PMCID: 4909931
PMID: 27292179
DOI: 10.1038/ncomms11768

[…] Alignment and quantitative analysis of electrophoretic traces was carried out in HiTRACE. To rigorously compare reactivities between different P5abc mutants, each RNA construct included the P5abc sequence flanked by 5′- and 3′-hairpins separated by single-stranded buffer regions. […]

library_books

Rich RNA Structure Landscapes Revealed by Mutate and Map Analysis

2015
PLoS Comput Biol
PMCID: 4643908
PMID: 26566145
DOI: 10.1371/journal.pcbi.1004473

[…] ethyl sulfate (DMS) was used in lieu of 1M7 since it yields a readily seen signal change across FMN concentrations [].Electrophoretic traces were aligned, baseline subtracted, and normalized with the HiTRACE MATLAB toolkit []. 1M7 modification traces were quantified, background subtracted, and corrected for attenuation using 10X dilutions, the unmodified controls, and the pentaloop hairpins added […]

Citations

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HiTRACE institution(s)
Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea; Bioinformatics Institute, Seoul National University, Seoul, Korea; Program in Biomedical Informatics, School of Medicine, Stanford University, Stanford CA, USA; Department of Biochemistry, Stanford University, Stanford, CA, USA; Department of Physics, Stanford University, Stanford, CA, USA
HiTRACE funding source(s)
Supported by National Research Foundation of Korea funded by the Ministry of Science, ICT and Future Planning [No. 2011-0009963 and No. 2012-R1A2A4A01008475]; a CONACyT pre-doctoral scholarship; Burroughs-Wellcome Foundation Career Award at the Scientific Interface for computational work and the National Institutes of Health [R01 GM102519].

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