SITECON plugin

SITECON - is a program pakage for recognition of potential transcription factor binding sites basing on the data about conservative conformational and physicochemical properties revealed on the basis of the binding sites sets analysis.

UGENE version of SITECON provides a tool for recognition of potential binding sites for over 90 types of transcription factors Also UGENE version of SITECON provides a tool for recognition of potential binding sites basing site alignment proposed by user. For the detailed method description check the original SITECON site

Citing SITECON

Please cite:

"Oshchepkov D.Y., Vityaev E.E., Grigorovich D.A., Ignatieva E.V., Khlebodarova T.M.SITECON:a tool for detecting conservative conformational and physicochemicalproperties in transcription factor binding site alignments and for siterecognition. // Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W208-12."

Data about used context-dependent conformational and physicochemical properties is available in the PROPERTY Database.

To search transcription factor binding sites in DNA sequence use "Analyze->Search TFBS with SITECON" menu:

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

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

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

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

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