SITECON: Searching Transcription Factor Binding Sites

To search for transcription factor binding sites in a DNA sequence, select the Analyze ‣ Search TFBS with SITECON… option from the context menu.

In the search dialog that appears, you must select a file with a TFBS profile. The profiles supplied with UGENE are located in the $UGENE/data/sitecon_models folder.

Once the profile is loaded, the threshold filter is populated with values read from the profile. You can use the filter to remove low-scoring regions from the results.

The regions found by the SITECON algorithm can be saved as annotations to the DNA sequence in Genbank format.

Every SITECON profile supplied with UGENE contains complete information about calibration settings provided to the UGENE team by the author of SITECON.

The original TFBS alignments used to calculate profiles can be requested directly from the author of SITECON.