antaRNA: ant colony-based RNA sequence design

Bioinformatics. 2015 Oct 1;31(19):3114-21. doi: 10.1093/bioinformatics/btv319. Epub 2015 May 27.


Motivation: RNA sequence design is studied at least as long as the classical folding problem. Although 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 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.

Availability and implementation: CONTACT:

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Ants / genetics*
  • Base Composition / genetics
  • Base Sequence
  • Databases, Genetic
  • Sequence Analysis, RNA / methods*
  • Software*