@article{Kleinkauf-web-2015,
author = {Kleinkauf, R. and Houwaart, T. and Backofen, R. and Mann, M.},
title = {{antaRNA} - Multi-objective inverse folding of pseudoknot {RNA} using ant-colony optimization},
journal = {BMC Bioinformatics},
volume = {16},
number = {1},
doi = {10.1186/s12859-015-0815-6},
pages = {1-7},
year = {2015},
user = {mmann},
issn = {1471-2105},
abstract = {
Background: Many functional RNA molecules fold into pseudoknot structures, which are
often essential for the formation of an RNA's 3D structure.
Currently the design of RNA molecules, which fold into a specific structure (known as RNA
inverse folding) within biotechnological applications, is lacking the feature of
incorporating pseudoknot structures into the design.
Hairpin-(H)- and kissing hairpin-(K)-type pseudoknots cover a
wide range of biologically functional pseudoknots and can be represented on a
secondary structure level.
Results: The RNA inverse folding program antaRNA, which takes secondary structure,
target GC-content and sequence constraints as input, is extended to
provide solutions for such H- and K-type pseudoknotted secondary structure
constraint.
We demonstrate the easy and flexible interchangeability of modules within the
antaRNA framework by incorporating pKiss as structure prediction tool capable of
predicting the mentioned pseudoknot types. The performance of the approach is
demonstrated on a subset of the Pseudobase++ dataset.
Conclusions:
This new service is available via a standalone version and is also part
of the Freiburg RNA Tools webservice. Furthermore, antaRNA is available
in Galaxy and is part of the RNA-workbench Docker image.
}
}