What tool can be used to predct regulatory element within an input sequence ?

Question

[Pei]

Hi all:

is there any tools that can be used to scan an input sequence and predict any potential regulatory element within that sequence?

in fact i got one such sequence (chicken) which was supposed to be bound by some regulator, e.g., TF, however, we are not sure what the exact regulator is?

so I guess that I may first try to identify the binding element within that sequence first, than experiment may go further to help detect that TF.

am I right ?

Thanks in advance!

[Joe]

The website http://www.softberry.com/ has lots of different prediction tools. Personally I think most of these kinds of prediction tools are pretty trash though, so proceed with caution.

[Pei]

Thank you jrj.healey ! I will have a check!

Answer 1

[Gautier Richard]

Your best chance is to use FIMO from the MEME suite and compare your sequence to the Chicken DNA Binding Protein Motifs Databases.

http://meme-suite.org/doc/fimo.html

I recommend using a Galaxy version of FIMO if you are not familiar with command-line tools.

One issue is that MEME doesn't have a Chicken DNA binding protein motifs database. Reading literature about motifs analyses in chicken might help you determine which database you need to use.