Publication

array(14 items)
   uid => 943 (integer)
   title => 'Comprehensive survey of conserved RNA secondary structures in full-genome al
      ignment of Hepatitis C Virus' (104 chars)
   abstract => 'Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically 
      infects liver hepatocytes and causes liver cirrhosis and cancer. These virus
      es replicate their genomes employing error-prone replicases. Thereby, they r
      outinely generate a large 'cloud' of RNA genomes (quasispecies) which-by tri
      al and error-comprehensively explore the sequence space available for functi
      onal RNA genomes that maintain the ability for efficient replication and imm
      une escape. In this context, it is important to identify which RNA secondary
       structures in the sequence space of the HCV genome are conserved, likely du
      e to functional requirements. Here, we provide the first genome-wide multipl
      e sequence alignment (MSA) with the prediction of RNA secondary structures t
      hroughout all representative full-length HCV genomes. We selected 57 represe
      ntative genomes by clustering all complete HCV genomes from the BV-BRC datab
      ase based on k-mer distributions and dimension reduction and adding RefSeq s
      equences. We include annotations of previously recognized features for easy 
      comparison to other studies. Our results indicate that mainly the core codin
      g region, the C-terminal NS5A region, and the NS5B region contain secondary 
      structure elements that are conserved beyond coding sequence requirements, i
      ndicating functionality on the RNA level. In contrast, the genome regions in
       between contain less highly conserved structures. The results provide a com
      plete description of all conserved RNA secondary structures and make clear t
      hat functionally important RNA secondary structures are present in certain H
      CV genome regions but are largely absent from other regions. Full-genome ali
      gnments of all branches of Hepacivirus C are provided in the supplement.' (1744 chars)
   authors => array(7 items)
      0 => array(3 items)
         last_name => 'Triebel' (7 chars)
         first_name => 'Sandra' (6 chars)
         sorting => 1 (integer)
      1 => array(3 items)
         last_name => 'Lamkiewicz' (10 chars)
         first_name => 'Kevin' (5 chars)
         sorting => 2 (integer)
      2 => array(3 items)
         last_name => 'Ontiveros' (9 chars)
         first_name => 'Nancy' (5 chars)
         sorting => 3 (integer)
      3 => array(3 items)
         last_name => 'Sweeney' (7 chars)
         first_name => 'Blake A' (7 chars)
         sorting => 4 (integer)
      4 => array(3 items)
         last_name => 'Stadler' (7 chars)
         first_name => 'Peter Florian' (13 chars)
         sorting => 5 (integer)
      5 => array(3 items)
         last_name => 'Petrov' (6 chars)
         first_name => 'Anton I' (7 chars)
         sorting => 6 (integer)
      6 => array(3 items)
         last_name => 'Marz' (4 chars)
         first_name => 'Manja' (5 chars)
         sorting => 7 (integer)
   type => '0' (1 chars)
   keywords => '' (0 chars)
   year => 2024 (integer)
   affiliation => 0 (integer)
   link_paper => '' (0 chars)
   link_supplements => '' (0 chars)
   file_published => 0 (integer)
   journal => 'Sci. Rep.' (9 chars)
   doi => ' 10.1038/s41598-024-62897-0' (27 chars)
   preprint => '-1' (2 chars)