TITLE:
Variant Map System to Simulate Complex Properties of DNA Interactions Using Binary Sequences
AUTHORS:
Jeffrey Zheng, Weiqiong Zhang, Jin Luo, Wei Zhou, Ruoyu Shen
KEYWORDS:
Pseudo-Random Number Generator; Stream Cipher; HC-256; Binary to DNA; Pseudo DNA Sequence; Large Noncoding; DNA Analysis; 2D Map; Visual Distribution; Variant Map System
JOURNAL NAME:
Advances in Pure Mathematics,
Vol.3 No.7A,
October
24,
2013
ABSTRACT: Stream cipher, DNA cryptography and DNA analysis are the most
important R&D fields in both Cryptography and Bioinformatics. HC-256 is an
emerged scheme as the new generation of stream ciphers for advanced network
security. From a random sequencing viewpoint, both sequences of HC-256 and real
DNA data may have intrinsic pseudo-random properties respectively. In a recent
decade, many DNA sequencing projects are developed on cells, plants and animals
over the world into huge DNA databases. Researchers notice that mammalian
genomes encode thousands of large noncoding RNAs (lncRNAs), interact with
chromatin regulatory complexes, and are thought to play a role in localizing
these complexes to target loci across the genome. It is a challenge target
using higher dimensional visualization tools to organize various complex interactive properties as visual maps. The Variant Map
System (VMS) as an emerging scheme is systematically proposed in this paper to apply multiple
maps that used four Meta symbols as same as DNA or RNA representations. System
architecture of key components and core mechanism on the VMS are described. Key
modules, equations and their I/O parameters are discussed. Applying the VM
System, two sets of real DNA sequences from both sample human (noncoding DNA)
and corn (coding DNA) genomes are collected in comparison with pseudo DNA sequences
generated by HC-256 to show their intrinsic properties in higher levels of
similar relationships among relevant DNA sequences on 2D maps. Sample 2D maps
are listed and their characteristics are illustrated under controllable environment.
Visual results are briefly analyzed to explore their intrinsic properties on
selected genome sequences.