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    Physico-chemical fingerprinting of RNA genes.

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    Authors
    Singh, A
    Mishra, A
    Khosravi, A
    Khandelwal, Garima
    Jayaram, B
    Affiliation
    Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
    Issue Date
    2016-12-08
    
    Metadata
    Show full item record
    Abstract
    We advance here a novel concept for characterizing different classes of RNA genes on the basis of physico-chemical properties of DNA sequences. As knowledge-based approaches could yield unsatisfactory outcomes due to limitations of training on available experimental data sets, alternative approaches that utilize properties intrinsic to DNA are needed to supplement training based methods and to eventually provide molecular insights into genome organization. Based on a comprehensive series of molecular dynamics simulations of Ascona B-DNA consortium, we extracted hydrogen bonding, stacking and solvation energies of all combinations of DNA sequences at the dinucleotide level and calculated these properties for different types of RNA genes. Considering ∼7.3 million mRNA, 255 524 tRNA, 40 649 rRNA (different subunits) and 5250 miRNA, 3747 snRNA, gene sequences from 9282 complete genome chromosomes of all prokaryotes and eukaryotes available at NCBI, we observed that physico-chemical properties of different functional units on genomic DNA differ in their signatures.
    Citation
    Physico-chemical fingerprinting of RNA genes. 2016, Nucleic Acids Res
    Journal
    Nucleic Acids Research
    URI
    http://hdl.handle.net/10541/620156
    DOI
    10.1093/nar/gkw1236
    PubMed ID
    27932456
    Type
    Article
    Language
    en
    ISSN
    1362-4962
    ae974a485f413a2113503eed53cd6c53
    10.1093/nar/gkw1236
    Scopus Count
    Collections
    All Paterson Institute for Cancer Research

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