RNA Base Triple Database Help

Table of contents

RNA Base Triple Database Help

About the database

Version history

Viewing triple families

Contact Info

About the database

The main page can be accessed at http://rna.bgsu.edu/Triples. The data are organized in two tables: 108 triple families on the left and 64 sequence combinations on the right. If a triple family or a sequence combination has been encountered in the Non-redundant list of RNA 3D structures, then the corresponding cell is colored green. If no instances have been observed in 3D structures, the cells are colored orange.

The numbers in the triple family table (9/36 for cWW-cHW triple family) refer to the number of observed sequence combinations (9 in this case) out of potential sequence combinations (36) that are predicted for this triple family. The maximum number of potential sequence combinations is 64, but in some families certain sequence combinations cannot form due to steric clashes.

The RNA Base Triple Database supports versioning, making it easy to access different releases independently. By default, the current version of the database is loaded (version 1.0 at the time of writing), but previous releases can be selected from the dropdown menu:

Version number is also clearly indicated in the urls of all pages to facilitate referencing, for example:

http://rna.bgsu.edu/Triples/triples.php?version=v1.0 or

http://rna.bgsu.edu/Triples/script.php?family=Triple_cWW_cHW&version=v1.0

Version history

v1.4 (current) - clashes are calculated between bases, sugars and backbones. More improvements in model building. August 20, 2011.

v1.3 - internal test release, new algorithm for backbone placement for model building.

v1.2 - internal test release.

v1.1 - minor modifications of v1.0. Triple_cWW_tSS family is now based on tsS subfamily of tSS base pair. Jan 25, 2011.

v1.0 - based on January 2011 Non-redundant dataset. Jan 15, 2011.

v0.9 - internal test release.

v0.8 - based on May 2010 Non-redundant dataset.

Versions can be compared via an online tool available at http://rna.bgsu.edu/Triples/compare.html

Viewing triple families

1 - the sequence combination may form, but only “near” examples have been observed meaning that one or more constituent basepair is classified as “near” by FR3D (llight-green background). Clicking on the “near” link will display these near instances on the same webpage. 

2 - the sequence combination can potentially form, but has never been observed (orange background).

3 - the sequence combination is not expected to form and has never been observed.

4 - the sequence combination is observed (dark green background).

Most elements on the page are clickable. For example, clicking on the number of clashes will bring up interactive KiNG applet, where the clashes are shown as red dots.

Clicking on the number of instances with show all instances using Jmol applet.

Note that the clashes have been calculated only for exemplars and predicted models. Thus, in case 1 on the picture above, the number of clashes refers to the model and not to the near instance. This is due to the fact that it may not be very useful to select a centroid from near instances and calculate its clashes because near instances can be quite diverse.

Both models and exemplars can be superimposed in the Jmol window on the right of the screen by clicking on checkboxes located next to sequence combinations in each cell.

Contact Info

Please email your questions or comments about the website to Anton Petrov (apetrov A T bgsu.edu).