Finding the common structure shared by two homologous RNAs

  title={Finding the common structure shared by two homologous RNAs},
  author={Olivier Perriquet and H{\'e}l{\`e}ne Touzet and Max Dauchet},
  volume={19 1},
MOTIVATION CARNAC is a new method for pairwise folding of RNA sequences. The program takes into account local similarity, stem energy, and covariations to produce the common folding. It can handle all RNA types, and has also been adapted to align a new homologous sequence along a reference structured sequence. RESULTS Using different data sets, we show that CARNAC provides a good partial prediction for a wide range of sequences (16S ssu rRNA, RNase P RNA, viruses) with only two sequences. In… CONTINUE READING