2.50
Hdl Handle:
http://hdl.handle.net/10541/620156
Title:
Physico-chemical fingerprinting of RNA genes.
Authors:
Singh, A; Mishra, A; Khosravi, A; Khandelwal, Garima; Jayaram, B
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.
Affiliation:
Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
Citation:
Physico-chemical fingerprinting of RNA genes. 2016, Nucleic Acids Res
Journal:
Nucleic Acids Research
Issue Date:
8-Dec-2016
URI:
http://hdl.handle.net/10541/620156
DOI:
10.1093/nar/gkw1236
PubMed ID:
27932456
Type:
Article
Language:
en
ISSN:
1362-4962
Appears in Collections:
All Paterson Institute for Cancer Research

Full metadata record

DC FieldValue Language
dc.contributor.authorSingh, Aen
dc.contributor.authorMishra, Aen
dc.contributor.authorKhosravi, Aen
dc.contributor.authorKhandelwal, Garimaen
dc.contributor.authorJayaram, Ben
dc.date.accessioned2017-02-15T12:55:32Z-
dc.date.available2017-02-15T12:55:32Z-
dc.date.issued2016-12-08-
dc.identifier.citationPhysico-chemical fingerprinting of RNA genes. 2016, Nucleic Acids Resen
dc.identifier.issn1362-4962-
dc.identifier.pmid27932456-
dc.identifier.doi10.1093/nar/gkw1236-
dc.identifier.urihttp://hdl.handle.net/10541/620156-
dc.description.abstractWe 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.en
dc.language.isoenen
dc.rightsArchived with thanks to Nucleic acids researchen
dc.titlePhysico-chemical fingerprinting of RNA genes.en
dc.typeArticleen
dc.contributor.departmentSupercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, Indiaen
dc.identifier.journalNucleic Acids Researchen
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