antaRNA - Ant Colony Based RNA Sequence Design
27.05.2015
Kleinkauf R, Mann M, Backofen R
Bioinformatics. 2015;31(19):3114-21.
Motivation: RNA sequence design is studied at least as long as the classical folding problem. While for the latter the functional fold of an RNA molecule is to be found, inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology, reliable RNA sequence design becomes a crucial step to generate novel biochemical components.
Results: In this article, the computational tool /antaRNA/ is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective guanine/cysteine (GC) content distribution, specific sequence constraints and additional fuzzy structure constraints. /antaRNA/ applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets.
