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🧬 PromKappa 1.0 makes Objective Digital Stains

Version 2.0 is available here: https://github.com/Gagniuc/PromKappa-2.0-makes-Objective-Digital-Stains

Version 3.0 is available here: https://github.com/Gagniuc/PromKappa-3.0-Objective-Digital-Stains-in-VB6

Description

PromKappa 1.0 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 the chart_comp folder), which can be later analyzed using different methods. 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 Homo sapiens (8515).txt) using the Open promoter file button. In the PromKappa case the Homo sapiens (8515).txt contains a series of gene promoters, as the analysis of gene promoters was the main aim of this application.

screenshot

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

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

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.