Using the CircleCompare Server

It is possible to download example CT files, to demonstrate the interface, by clicking on the links above the "Select CT Input" form section.

  1. Select a predicted CT structure for analysis.

    A CT file can be uploaded using the "Select Predicted CT File" control. The length of the sequence that creates the predicted structure(s) must be equal to the length of the sequence contained in the accepted structure. This CT file can have any number of structures in it.
  2. Select an accepted CT structure for analysis.

    A CT file can be uploaded using the "Select Accepted CT File" control. This CT file must have only one structure in it.
  3. Add optional data, if desired.

    The CircleCompare server allows SHAPE annotation, by uploading a SHAPE data file with the "Select SHAPE Annotation File" control.
  4. Enter an email address where results can be sent, if desired.

    If an email address is specified in the appropriate box, an email will be sent to inform you when calculations are done. Note that failing to enter an email address may cause results to be inaccessible, if you navigate away from the server while calculations are running.
  5. Begin the calculation.

    Press the "Submit Query" button to begin the calculation. If you remain on the server page, the results will appear when they are finished.

Notes Concerning Web and Downloadable Images

All images generated from the CircleCompare interface color-code pairs between nucleotides to clarify which structure(s) the pair is found in. The color scheme is as follows:
Green: Pair Present in Predicted and Accepted Structure
Red: Pair Present in Accepted Structure Only
Black: Pair Present in Accepted Structure Only

All downloaded files except SVG include detailed information on the comparison between the structures, including sensitivity, positive predictive value, number of pairs, and number of pseudoknotted pairs.

For detailed explanations of the CircleCompare algorithm and its parameters, please click here.