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Table 5 Motif Searches in Swellix Analysis of HERV RNA

From: Swellix: a computational tool to explore RNA conformational space

Motif % occurrence
GNRA tetraloop WWWGNRAWWW (((....))) 0.00
Hepatitis C 1 WWGAACUACWW_WWGCWW (((.....(((_)))))) 4.41
Hepatitis C 2 WWUACCCACCWW_WWGAGWW (((......(((_))).))) 2.71
HIV TAR WWAUCUGWW_WWCUWW (((...(((_)))))) 4.58
HIV and 7SK WWUCUUWW_WWARWW (((..(((_)))))) 0.73
HIV RRE 1 WWUGGAAWW_WWUGGGAGWW (((...(((_)))....))) 2.80
HIV RRE 2 WWGGGCWW_WWGGUACWW (((..(((_)))...))) 4.58
  1. A 141-nucleotide Human Endogenous Retroviral (HERV) RNA sequence (Genbank # AY944072.1)was folded using a phase 1 parallelized Swellix on the Blue Waters XE nodes with 16 cores per node. The computation generated 643 components and 12,518,055,094 bundled structures in an average runtime of 23,951 s. The minimum helix length constraint is 3. The motifs that were counted are RNA loops, some of which bind small molecule drugs in HIV Trans Activating Response (TAR) or Rev. Responsive Elements (RRE), 7SK RNA, or Hepatitis C RNA [32,33,34,35,36,37]. For the motif sequence, W indicates a Watson-Crick pair; N indicates any nucleotide; and R indicates a purine. In the sequence and dot and parentheses notation, an underscore indicates any variable number of intervening nucleotides. The percent occurence is the number of times the motif was counted during the computation divided by the total number of structures generated