ShapeSorter

ShapeSorter
A method for detecting conserved RNA structure features that are supported by experimental SHAPE-evidence

Citation

Volodymyr Tsybulskyi, Irmtraud M Meyer, ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence, Nucleic Acids Research, 2022 doi: doi.org/10.1093/nar/gkac405

Download Program & Example Data

Software:

ShapeSorter V1
In order to compile software, you have to install PHY library

You also can use already compiled singularity container for execution without any required package installation:

Singularity Image

Output Format

What am I looking at?

Each row represents one helix predicted by the pipeline along with various statistics as described below.

What does each column mean? (Brackets indicate corresponding column only present in downloadable output)

Pvalue: Significance of the result. Technically the fraction of randomly generated helices with a LogLikelihood score greater than the helix in question.
LogLikelihood: (LogLikeRatio) The likelihood that the helix is conserved, computed using the Felsenstein algorithm. See citation for details.
LogLikeRatioShape The likelihood that the helix is conserved, computed using the combined model of Felsenstein and DFG algorithms. See citation for details.
(PairedLogLikelihood): Likelihood that bases in helix evolved in a paired manner
(UnpairedLogLikelihood): Likelihood that bases in helix evolved in an independent unpaired manner
MeanFracCanonicalBP: Mean percentage that basepairs in the helix are canonical, i.e. Watson-Crick or wobble base.
Covariance: Phylogeny-free measurement of compensatory mutations.
Conservation: Percent identity of nucleotides in the helix
HelixLength: Number of basepairs in helix.
(AlignmentSize): Number of species in alignment
(AlignmentLength): Width of the alignment
(TreeLength): Sum of all branch lengths for the input phylogeny tree
(Structure): Dotbracket structure (0 unless enabled via Advanced Options)
Bps: Tuples respresenting basepaired positions (where the first base is 0)

Disclaimer

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.