TF binding site

[Shah, Mohd (NIH/NEI) [F]]

Hello,

I hope this email finds you well. I am Mohd Hussain Shah, working as Postdoc at NEI/NIH.  I am currently working on transcription factor binding site analysis and would like to know if position-specific scoring matrices (PSSMs) are the best approach, or if there are other software tools you would recommend for this purpose. I typically work with chick data, so any resources or recommendations specific to this model organism would be highly appreciated.

If you have any tutorials or guides on how to use these tools effectively, I would be grateful if you could share them with me.

Thank you for your time and assistance.

Sincerely,
Hussain