Select task to perform
Start HMM-based method of finding transcription factor binding sites. You will have to input the set of experimentally determined binding site sequences; all sequences must be of the same length. Optionally, you can also specify the PFM of the factor's matrix - it is wise to do so when the number of sequences used to produce the matrix is higher, than the number of sequences you can provide to the program. If you input both matrix and sequences, please ensure that PFM column sum is equal to the length of any of the sequences.
If you already ran some TFBS searches at COTRASIF, then you can compare two results using the orthology data from the current release of Ensembl. For example, to find out in the promoters of which genes is the ISRE TFBS preserved between rat and mouse, you would have to run first the analysis on rat (using either method), then run the analysis on mouse, and then use the button above to compare two results. As a result of comparison, you will get the list of genes for each of the organisms of the compared pair, where the TFBS was found in the promoter.