PWM Scan For Toxoplasma gondii

Question

[mercadocapote]

I want to find a PWM-motif that is present in promoter regions of Toxoplasma gondii. I basically want to see the presence of specific DNA sequence [PWM-motif] in the promoter region which I obtained using transcription factors (protein) - DNA interaction studies, Protein Binding Microarray [PBM].

What can you recommend? (Programs, Packages, Databases, Advice)

Answer 1

[Kamil]

Check out the MEME suite for software to scan sequences for PWM sites.

CISBP is a nice motif database, but none of the 219 TFs for Toxoplasma gondii seem to have high quality supporting evidence.