TFBS Footprinting

Identification of cis-regulatory elements


Input:

Ensembl transcript id(s)

Desired promoter length (e.g. 1000)

Jaspar database TFBSs

 

Process:

Retrieve orthologous mammal sequences from Ensembl database

Generate dinucleotide weight matrices from Jaspar TFBSs

Score each mammal sequence using weight matrices

Perform statistical alignment of orthologous sequences

Identify predicted human TFBSs conserved across multiple species

 

Output:

Figure(s) of human promoter with top 10 scoring predicted TFBSs