ИСТИНА

A usual way to determine the evolutionary relatedness, or homology, of two DNA sequences is to search for traces of sequence conservation. However the lack of sequence conservation does not necessarily mean the lack of homology. Not detectable at the primary sequence level, it can be inferred when moving to the level of DNA/RNA secondary structures, which were shown to play an important role in many processes of genome functioning. Here we implemented DNAStructProfiler, an automated pipeline for reconstruction of DNA/RNA secondary structure conservation profiles that will allow researchers to reveal position-­‐specific secondary structures in a set of DNA sequences. The tool can be used with any program that searches for DNA/RNA secondary structures, such as stem-­‐loops, quadruplexes, triplex DNA, and any other structures of interest and is freely available at www.dnapunctuation.org/DNAStructProfiler.html. We demonstrate how the tool can be used to reveal evolutionary conserved stem-­‐loop structures in human L1 retrotransposons.