RNApuzzler v1.0

Motivation: RNA secondary structure has emerged as most useful representation for
studying the function of RNA.  It captures the dominating of the free
energy of RNA folding.  Using empirically determined energy parameters,
these secondary structures of nucleic acids can be efficiently computed by
recursive algorithms.  Several software packages supporting this task are
readily available. As RNA secondary structures are outerplanar graphs, they
can be drawn without intersection in the plane.  Interpretation by the
practitioner is eased, when these drawings conform to a series of
constraints that include outerplanarity. These constraints are the reason
why RNA drawing is difficult. Many RNA drawing algorithms do not always
produce intersection-free (outerplanar) drawings.
Results: To remedy this shortcoming, we propose here the RNApuzzler algorithm, which is guaranteed
to produce intersection-free drawings. It is based on a drawing algorithm
respecting constraints based on nucleotide distances (RNAturtle).  We
investigate relaxations of these constraints allowing for intersection-free
drawings.  Based on these relaxations we implemented a fully automated,
simple, and robust algorithm that produces aesthetic drawings adhering to
previously established guidelines.  We tested our algorithm using the RFAM
database and found that we can compute intersection-free drawings of all
RNAs therein efficiently.



RNApuzzler is implemented within the ViennaRNA Package v2.35. Therefore, it will be built during the ViennaRNA build process. The following steps must be performed under Linux to create a binary of RNApuzzler:

./autogen.sh

./configure --without-perl --without-python --without-doc --without-forester --without-kinfold --without-kinwalker

make

make install

ViennaRNA v2.35 is now globally installed on the system. If you want to build under MacOS, please note further information in the file INSTALL.



The following commands are used to create drawings with RNApuzzler or RNAturtle:

cat folded-rna-seq.txt | RNAplot -t 4 <- RNAplot draws with the RNApuzzler algorithm
cat folded-rna-seq.txt | RNAplot -t 3 <- RNAplot draws with the RNAturtle algorithm

Further layout parameters can be accessed with:

RNAplot -h