[BioC] Help on Cosmo

[Prashantha Hebbar Kiradi [MU-MLSC]]

Dear Friends,

I am interested in finding the consensus sequence of Transcription factor binding sites of list probe sequences. I found that cosmo would be the best choice. But while going through cosmo vignette, I did not understand selection criteria to choose sequences for calculation of background model. I mean to say, If probe sequences are of promoter region, should sequences to be selected to calculate the back ground model, also be promoter sequences of the same(and of the same organism)probes?

Thanking you in anticipation.

Regards,

Prashantha
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