Predicted target genes - which tools are the best to use?

Question

[JJ]

Hi,

I am new to TF motif search so I would very much appreciate it if you could point me to the best tools to identify binding sites in the genome to predict target genes using published motifs. The MEME suite would be my current choice - or do you have other recommendations?

I am interested in two things:

1. use a number of motifs that were published for a given factor to predict target genes

2. use motifs from (1) as well as the motifs from 2-3 other factors that could be present as well to predict target genes

I would also like to be able to set the search space - so the upstream and downstream region where the tool should look to identify the target genes. I have the motifs as PWM or sequence logos (I found a tool though that can convert the logos to PWMs).

Thank you for your advice

Answer 1

[Kevin Blighe]

Take a look also at JASPAR and TRANSFAC