Question: Consensus motif of closely related TFs
0
gravatar for rbronste
23 months ago by
rbronste360
rbronste360 wrote:

Hi I am wondering whether there are any good approaches for creating a census motif from a number of TFs in the same family, that are very closely related. For instance from Hox TFs or ZNFs, so if you have PWMs for individual members what is the best way to go about creating a consensus sequence? Thanks!

ADD COMMENTlink modified 21 months ago by UnivStudent380 • written 23 months ago by rbronste360
1
gravatar for simon.vanheeringen
22 months ago by
simon.vanheeringen200 wrote:

You can cluster the PWMs.

One option is to use GimmeMotifs (disclaimer: I wrote the software). The command gimme cluster can be used. There are also other tools that can do this, such as RSAT.

ADD COMMENTlink written 22 months ago by simon.vanheeringen200
0
gravatar for goodez
23 months ago by
goodez480
United States
goodez480 wrote:

Do you want to make a sequence logo? You can do that easily through a web browser: http://weblogo.threeplusone.com/create.cgi

You can also do it with command line tools. Or are you trying to do something different?

ADD COMMENTlink written 23 months ago by goodez480

No actually its not just the logo, trying to figure out how to combine the PWM information from the different closely related motifs into one consensus motif.

ADD REPLYlink written 23 months ago by rbronste360
0
gravatar for UnivStudent
21 months ago by
UnivStudent380
Canada
UnivStudent380 wrote:

I've also used PWMclus in "CCAT: Combinatorial Code Analysis Tool for transcriptional regulation." for a task like this with good results. I will warn that this type of analysis wouldn't work well for many families (especially Zinc Fingers) with very diverse motifs if you choose a single consensus motif. You have to choose 1 consensus per cluster.

ADD COMMENTlink written 21 months ago by UnivStudent380
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