CorreLogo Submission Form: example tRNA


All you probably have to do in order to run this example is to click "Submit Query" at the bottom of this page. If you want to run your own set of sequences or you want to customize the output, enter values into the sections one to three of the form below (sections 2 and 3 are optional). For more detailed information consult our help page.

Background of example sequences:

The sequences provided in this example correspond to the tRNA. The alignment is derived from the Rfam entry of tRNA. In order to obtain a simple example, the original Rfam seed alignment with 1114 sequence was modified: the alignment was "collapsed" with respect to the Saccharomyces cerevisiae PHE-tRNA sequence (K01553.1) (this means that all columns corresponding to a gap in that sequence were removed). Please note that this example is "large": the default parameters work fine for the systems we tested, but if you specify a lower cutoff below 0.1 bits, you might experience problems with both JVX and VRML due to browser/viewer limitations with respect to the maximum number of displayable polygons. In this case it helps to reduce the number of polygons by using a smart choice of options (no 3D logo characters, no 2D sequence logo, option "Optimize for 3D printing" activated). MS Internet Explorer was in our experience the most "resilient" when it comes to displaying large models with the used applet. Another possibility is to download the generated JVX or VRML files and view them with standalone programs (like the JavaView standalone application).

3. Customize generated output (optional)

Note to the user regarding default max and min values: The default settings are currently set to give the user an idea of what the output looks like. However, the user should feel free to alter these values to change the resolution of the results i.e. how much noise should be included in the answer which may obscure, for example lower stacks if max is set too high. Please also see help information for further details.