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🧬PromKappa 2.0 makes Objective Digital Stains

PromKappa 2.0 is a complete application made in Visual Basic 6.0 (VB6) that generates Objective Digital Stains (aka DNA patterns). The main output of the application consists of a series of images that are saved in the chart folder (or chart_comp folder), which can be later analyzed using different methods. A second output can be the results.htm file which contains a series of measurements for each ODS generated by the application. Note that if you are familiar with python, then VB6 will come natural to you. Also, note that once the application is started, the first step will be to load a FASTA file (the gene_promoters_complete.fa) using the Open promoter file button. In the PromKappa case the gene_promoters_complete.fa contains a series of gene promoters, as the analysis of gene promoters was the main aim of this application.

The compiled version of PromKappa (PromKappa.exe) will ask for a dependency file called msvbvm60.dll and possibly other dependency files. These files are present in the bin folder. The following files are a complete set of dependencies that a regular VB6 app may require:

  • msvbvm60.DLL
  • VBA6.DLL
  • shlwapi.dll
  • MSCOMCTL.OCX
  • COMDLG32.OCX

However, if you install Visual Basic 6.0 from the Visual Studio 6.0 package, then all dependency files will be present on your system by default.

📁 Implementations - other

The Objective Digital Stains are also implemented in two scripting languages, from which an entire customised application can be made.

In Java Script: https://github.com/Gagniuc/Objective-Digital-Stains

In PHP: https://github.com/Gagniuc/Objective-Digital-Stains-in-PHP

📁 Info on ODSs

Please read more about DNA patterns (aka Objective Digital Stains) here:

Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters:

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-512

Gene promoters show chromosome-specificity and reveal chromosome territories in humans:

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-278

Algorithms in Bioinformatics: Theory and Implementation:

https://www.wiley.com/en-ag/Algorithms+in+Bioinformatics%3A+Theory+and+Implementation-p-9781119697961

📁 Screenshot

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References

  • Gagniuc P.A. and Ionescu-Tirgoviste C.: Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics 2012, 13:512.

  • Ionescu-Tîrgovişte C*, Gagniuc PA*, Guja C (2015) Structural Properties of Gene Promoters Highlight More than Two Phenotypes of Diabetes. PLoS ONE 10(9): e0137950.

  • Gagniuc P.A. and Ionescu-Tîrgovişte C. Gene promoters show chromosome specificity and reveal chromosome territories in humans, BMC Genomics 2013, 14:278.

  • Paul A. Gagniuc. Algorithms in Bioinformatics: Theory and Implementation. John Wiley & Sons, Hoboken, NJ, USA, 2021, ISBN: 9781119697961.