Citation

Wiebe NJ, Meyer IM. (2010) TRANSAT--A method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures. PLoS Comput Biol. 6 (6): e1000823. doi:10.1371/journal.pcbi.1000823

Download Program & Example Data

We release two versions of Transat here, the first version (v1) is the original work developed and evaluated in the above citation, kept here for reproducibility purposes. The second version (v2) is a highly optimized version of the original work that has undergone some major interface changes to make them incompatible, but results should be identical in theory. The second version (v2) is what is currently being run on the webserver, and should be the one used if reproducing the web server commands and results are desired.

Transat v1 (Wiebe & Meyer 2010)

• Transat program (tar-ball), or clone our git repository here
• Transat input and output files for the hok data set (tar-ball)
• Transat input and output files for the trp-attenuator data set (tar-ball)
• Transat input and output files for the artificial data and the rfam set are too large to be made available here. Please contact us (below), if you are interested.

Transat v2

• Transat v2 source (tar-ball)

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.
• (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.