The objective digital stain (ODS) is represented by a distribution of points on a two-dimensional (2D) image, which reflects the information structure inside a DNA/RNA sequence. In turn, the shape of the distribution pushes the association of the method with a kind of “digital stain”, thus safely establishing the name of the method. In the past, ODSs were simply called DNA patterns. On ODSs, the information content (IC) is represented vertically on the y-axis and the frequency of different letters is represented horizontally on the x-axis. The overall idea surrounding this method is that similar distributions of two or more DNA/RNA sequences may show similar functions. Interestingly, dissimilar DNA/RNA sequences may show similar ODSs. This intriguing proprietary has been demonstrated repeatedly over time. The first observation was made in 2012 in the journal BMC Genomics. There, different ODS patterns have been shown for eukaryotic gene promoters that indicate several generic classes of promoters (more than 10 classes of promoters in eukaryotes). Moreover, in 2013 in the same journal, a correlation was made between chromosomal territories and ODS patterns shown by gene promoters. More recently, in 2015, a publication in the journal PLoS ONE showed the connection between ODSs of promoter sequences and the genes associated with type 1 and 2 diabetes. This latest publication showed more clearly that ODSs are able to link the DNA sequence characteristics to different biological functions.
Live demo: https://gagniuc.github.io/Objective-Digital-Stains/
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Paul A. Gagniuc. Algorithms in Bioinformatics: Theory and Implementation. John Wiley & Sons, Hoboken, NJ, USA, 2021, ISBN: 9781119697961.
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Gagniuc and Ionescu-Tirgoviste: Gene promoters show chromosome-specificity and reveal chromosome territories in humans. BMC Genomics 2013 14:278.
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Gagniuc and Ionescu-Tirgoviste: Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics 2012 13:512.
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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.