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 ...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.展开更多
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 encoding thousands of large noncoding RNAs ...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 encoding 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 tools to organize various complex interactive properties as visual maps. In this paper, a Pseudo DNA Variant MapPDVM is proposed following Cellular Automata to represent multiple maps that use four Meta symbols as well as DNA or RNA representations. The system architecture of key components and the core mechanism on the PDVM are described. Key modules, equations and their I/O parameters are discussed. Applying the PDVM, two sets of real DNA sequences from both the sample human (noncoding DNA) and corn (coding DNA) genomes are collected in comparison with two sets of pseudo DNA sequences generated by a stream cipher HC-256 under different modes 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 a controllable environment. Various distributions can be observed on both noncoding and coding conditions from their symmetric properties on 2D maps.展开更多
文摘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.
文摘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 encoding 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 tools to organize various complex interactive properties as visual maps. In this paper, a Pseudo DNA Variant MapPDVM is proposed following Cellular Automata to represent multiple maps that use four Meta symbols as well as DNA or RNA representations. The system architecture of key components and the core mechanism on the PDVM are described. Key modules, equations and their I/O parameters are discussed. Applying the PDVM, two sets of real DNA sequences from both the sample human (noncoding DNA) and corn (coding DNA) genomes are collected in comparison with two sets of pseudo DNA sequences generated by a stream cipher HC-256 under different modes 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 a controllable environment. Various distributions can be observed on both noncoding and coding conditions from their symmetric properties on 2D maps.
