Dear Bioconductor community, we developed a package for detecting potential intramolecular triplex patterns in DNA sequence (http://www.bioconductor.org/packages/release/bioc/html/triplex.html) and we're going to review the sensitivity and specificity measures of the detection algorithm. But we are doubtful what is actually the right way to do that, I mean how should we generate random testing DNA sequences to get relevant results? We found some articles citing the uShuffle tool (http://digital.cs.usu.edu/~mjiang/ushuffle/) so that might be the direction. But we are curious if someone from Bioconductor community has some other experiences with solving this problem. We would be really thankful for that. So what tools do you use for this purpose? And what sequence properties (k-let counts, etc.) you think should be preserved? Thank you a lot, Jiri Hon