Abstract
RNA splicing normally generates stable splice- junction sequences in viruses that are important in the context of virus mimicry. Potential variability in envelop proteins may occur with point-mutations inducing cryptic splice-junctions, which would remain unrecognized by T-memory cells of higher organisms in vaccine trials. Such aberrant splice- junctions result from evolution-specific non-conser- vation of actual splice-junction sites due to mutations; as such, locations of splice-junctions in a test DNA sequence could only be imprecisely specified. Such impreciseness of splice-junction locations (or cryptic sites) in a sequence is evaluated in this study via “noisy” attributes (with associated stochastics) to the mutated subspace; and, relevant fuzzy considerations are invoked with membership attributes expressed in terms of a spatial signal-to-noise ratio (SSNR). That is, SSNR adopted as a membership function expresses the belongingness of a site-region to exon/intron subspaces. An illustrative example with actual (Dengue 1 viral) DNA data is furnished demonstrating the pursuit developed in predicting aberrant splice-junctions at cryptic sites in the test sequence.
Highlights
Eukaryotic genomic data encoded via spatial statistical occurrence of the nucleotide set {A, T, C, G} eventually translates into a protein complex through transcription and translation processes
Potential variability in envelop proteins may occur with point-mutations inducing cryptic splice-junctions, which would remain unrecognized by T-memory cells of higher organisms in vaccine trials
Such impreciseness of splice-junction locations in a sequence is evaluated in this study via “noisy” attributes to the mutated subspace; and, relevant fuzzy considerations are invoked with membership attributes expressed in terms of a spatial signal-to-noise ratio (SSNR)
Summary
Eukaryotic genomic data encoded via spatial statistical occurrence of the nucleotide set {A, T, C, G} eventually translates into a protein complex through transcription and translation processes. Among feasible techniques developed in ascertaining the delineation of codon/noncodon parts, (that is, in locating the splice-junctions), indicated in [3] is an entropy estimator method that extracts “meaningful signal” from the exon/intron segments of a test DNA; and an entropy technique is applied to detect the underlying splice-junctions between the segments This is, an information-theoretic (or entropy-based) tool envisaged in a classical setting. The thematics of the present study refers to developing an appropriate FIE that delineates fuzzy overlaps of codon/non-codon parts so as to elucidate the underlying cryptic (or aberrant) splice-junctions This is done on the basis of SSNR defined with reference to the spatial-jitter.
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