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"Humanities and Science University Journal" №24 (Physical and mathematical, biological and technical science), 2016

DNAStructProfi ler: An Automated Pipeline for Reconstruction of DNA/RNA Secondary Structures Conservation Profi les

M. S. Poptsova, D.A. Grechishnikova
Price: 50 руб.
 A usual way to determine the evolutionary relatedness, or homology, of two DNA sequences is to search for the traces of sequence conservation. However, the lack of sequence conservation does not necessarily mean the lack of homology. Since the homology is not detectable at the primary sequence level, it can be inferred when moving to the level of DNA/RNA secondary structures that are known to play an important role in many processes of genome functioning. Here, we implemented the DNAStructProfi ler, an automated pipeline to reconstruct DNA/RNA secondary structures conservation profi les that will allow researchers to reveal position-specifi c secondary structures in a set of DNA sequences. We demonstrate how the tool can be used to reveal evolutionary conserved stem-loop structures in human L1 retrotransposons.
Keywords: DNA/RNA Secondary Structures Conservation Profi le, stem-loop, L1, LINE retrotransposons, dynamic programming.
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