Abstract:
:Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional properties of non-coding RNAs. In this paper, we introduce a formal framework to combine the biochemical signal collected from MaM experiments, with the evolutionary information available in multiple sequence alignments. We apply neutral theory principles to detect complex long-range dependencies between nucleotides of a single stranded RNA, and implement these ideas into a software called aRNhAck We illustrate the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA-RNA, RNA-protein, RNA-DNA and RNA-ligand interfaces. aRNhAck is freely available at http://csb.cs.mcgill.ca/arnhack.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Reinharz V,Ponty Y,Waldispühl Jdoi
10.1093/nar/gkw217subject
Has Abstractpub_date
2016-06-20 00:00:00pages
e104issue
11eissn
0305-1048issn
1362-4962pii
gkw217journal_volume
44pub_type
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