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

antaRNA: ant colony-based RNA sequence design.

Author information

1
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
2
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany, Center for Biological Signaling Studies (BIOSS), University of Freiburg, Germany, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

Abstract

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:

http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26023105
PMCID:
PMC4576691
DOI:
10.1093/bioinformatics/btv319
[Indexed for MEDLINE]
Free PMC Article

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