Variant Map Construction to Detect Symmetric Properties of Genomes on 2D Distributions
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Supplementary material
Other Title
Authors
Zheng, Jeffrey
Zhang, Weiqiong
Luo, Jin
Zhou, Wei
Liesaputra, Veronica
Zhang, Weiqiong
Luo, Jin
Zhou, Wei
Liesaputra, Veronica
Author ORCID Profiles (clickable)
Degree
Grantor
Date
2014
Supervisors
Type
Journal Article
Ngā Upoko Tukutuku (Māori subject headings)
Keyword
symmetric property
genomic sequence
partition
segment
measurement
2D maps
visual distribution
variant map construction
genomic sequence
partition
segment
measurement
2D maps
visual distribution
variant map construction
ANZSRC Field of Research Code (2020)
Citation
Zheng, J., Zhang, W., Jin, L., Wei, Z., and Liesaputra, V. (2014). Variant Map Construction to Detect Symmetric Properties of Genomes on 2D Distributions. Journal of Data Mining in Genomics & Proteomics, 5(1)http://dx.doi.org/10.4172/2153-0602.1000150
Abstract
Visualization Methods have played a key role in the Human Genome Project. After further development in other international projects such as ENCODE, larger numbers of Genome Databases are established and mass Genome- wide gene expression measurements are developed. In current situation, it is necessary to shift targets in computational cell biology from collecting sequential data to making higher-level interpretation and exploring efficient content-based retrieval mechanism for genomes. Mammalian genomes encode thousands of large non-coding RNAs (lncRNAs), many of which regulate gene expression, interact with chromatin regulatory complexes, and are thought to play a role in localizing these complexes to target loci across the genome. Using higher dimensional visualization tools, their complex interactive properties could be organized as different visual maps. The Variant Map Construction VMC as an emerging scheme is systematically proposed in this paper to apply multiple maps that uses four Meta symbols as same as DNA or RNA representations. System architecture of key components and core mechanism on the VMC are described. Key modules, relevant equations and their I/O parameters are discussed. Using the VMC system, two DNA data sets of multiple real sequences are tested to show their visible properties in higher levels of intrinsic relationships among relevant DNA sequences in 2D maps. Visual results are briefly analyzed to explore their intrinsic properties and symmetric characteristics on relevant genome sequences under 2D maps of the Variant Map Construction. A set of sample 2D maps are included and their characteristics are illustrated under various controllable environment.
Publisher
OMICS Group
Permanent link
Link to ePress publication
DOI
doi:10.4172/2153-0602.1000150
Copyright holder
OMICS Group
Copyright notice
JDMGP, an open access journal