ShapeFinder specifications

Information


Unique identifier OMICS_25398
Name ShapeFinder
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Programming languages Objective-C
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes

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Publication for ShapeFinder

ShapeFinder in publications

 (43)
PMCID: 5853050
PMID: 29540207
DOI: 10.1186/s12977-018-0407-4

[…] precipitation after 45 min incubation at 37 °c and reverse transcribed as described previously. samples were analyzed by capillary electrophoresis in an abi 3730 xl sequencer and quantified with shapefinder software []. data were normalized as described previously []. outliers were defined as above and were removed from the dataset. these constituted less than 8% of values. the average […]

PMCID: 5946862
PMID: 29390080
DOI: 10.1093/nar/gky033

[…] integrate peaks. the code for this application (which we call robfinder) is freely available on github, at https://github.com/rnaplus/robfinder. we also have used other software packages (including shapefinder () and qushape ()) to process capillary electrophoresis data, with similar results., to process a dataset using robfinder, the raw fluorescence intensities for the size-standard ladder […]

PMCID: 5784592
PMID: 29368653
DOI: 10.1186/s12977-018-0393-6

[…] the make and model to be used. several programs are available for analysis; some of these necessitate the use of particular fluorophores. the first of the analysis programmes to be established, shapefinder software is mac-specific and is rigid in its interpretation of each wavelength, necessitating the use of sets such as 6fam, vic, ned and pet on an applied biosystems instrument, to run […]

PMCID: 5678188
PMID: 29118447
DOI: 10.1038/s41598-017-15317-5

[…] and 6-tamra there were prepared ddntp ladders: (most often ddgtp and ddatp). cdna fragments were separated by capillary electrophoresis (dna research center, poznan)., data were analyzed with the shapefinder program. quantitative nmia reactivities for individual datasets were normalized to a scale in which 0 indicates an unreactive site and the average intensity at highly reactive sites […]

PMCID: 5591316
PMID: 28887451
DOI: 10.1038/s41467-017-00536-1

[…] on a beckman ceq-8000 with a d3-labeled library from unmodified rna, an ir800-labeled ddctp sequencing ladder, and a d2-labeled ddgtp sequencing ladder. the raw ceq traces were processed with shapefinder to determine peak areas for each 5′ domain nucleotide. after background subtraction, the peak areas were scaled such that the average of the 92–97 percentile peak areas equaled 100. […]


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ShapeFinder institution(s)
Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
ShapeFinder funding source(s)
Supported by the U.S. National Institutes of Health (AI068462).

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