An architecture-independent algorithm for microRNA target prediction

Natalya Fokina¹, Alexander Grinev^2
1Moscow State Medical University, retrospector@ispras.ru
²Moscow State Medical University, grinev.ab@1msmu.ru

Nowadays the research on RNA interference is a subject of growing interest. One of the most perspective directions of this research is the use of bioinformatics methods to predict possible interactions of microRNAs with their mRNA counterparts, which allows to increase the accuracy and efficiency of their confirmation using laboratory means. In spite of this fact, the existing tools are unable to meet all the needs of molecular biology. An example of a problem currently lacking an appropriate solution is the study of RNA interference between organisms belonging to different taxonomic groups, notably, in parasite-host systems. Parasites utilise the host cell as a source of nutrients and habitat; molecular genetic profiles of both participants of this interaction are subject to dynamic changes. In this paper we present a novel algorithm for detection of interactions involving RNA molecules in a wide range of organisms. The proposed solution exceeds the existing ones in several characteristics and, in our view, can be broadly used in molecular biology and bioinformatics.