I have no background in bioinformatics, I don't know how to write a script, I can just use a pipette and do some stuff on the bench, so I would need someone who can help me to find some motif in a genome..
Here is the idea, I am working on 2 t-box genes in Caenorhabditis elegans. It is quite accepted that most of the t-box proteins bind to DNA with almost the same motif. This motif is known, the PWM is known. So I would like to use these elements to scan the entire C.elegans genome.
As output, I would like to have a list of putative binding site, with their positions (if they are in 5' region, intron, 3' region etc etc) and if they could be real or not.
I would like this result to see if already from such analysis we can see some trends in the genome.
I heard that the best tools to make such analysis is the Meme suite, I tried by my own to use it but I always have some errors in everything I try.
So if someone could help me to do this analysis it could be amazing !