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Farach, M., Noordewier, M., Savari, S., Shepp, L., Wyner A. and Ziv, J. (1995) On the entropy of DNA: Algorithms and measurements based on memory and rapid convergence. Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA’95), San Francisco, January 1995, 48-57.

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• TITLE: Fuzzy splicing in precursor-mRNA sequences: prediction of aberrant splice-junctions in viral DNA context

  AUTHORS: Perambur S. Neelakanta, Sharmistha Chatterjee, Mirjana Pavlovic, Abijit Pandya, Dolores de Groff

  KEYWORDS: DNA; Exon/intron; Aberrant/Cryptic Splice–Junction; MRNA Sequence; Fuzzy Subspace; Spatial SNR

  JOURNAL NAME: Journal of Biomedical Science and Engineering, Vol.4 No.4, April 22, 2011

  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.