Binding Site Matrices.

Question

[pixie@bioinfo]

I have gathered couple of binding site sequences of c-fos and c-jun for human, rat and mouse. I will have to generate matrices and map them to the promoter region of a human gene. Kindly tell me how I should be doing it and which are the softwares that I should be using....

[Khader Shameer]

Please take a look at a related question on mouse regulatory motifs posted by Andrew.

Answer 1

[Stew]

A good place to start is the RSAT web tools. Once you have matrices you can use the sequence retrieval tools to get the promoter sequence of your gene(s) of interest. Then you can use the pattern matching tools (matrix-scan and patser) to search for occurrences within your promoter. The feature map tools can then be used to generate a figure showing their location. Hope that helps.