Question: Transcription factor binding on DHS sites
0
gravatar for efthimis_g
5.4 years ago by
efthimis_g0
Greece
efthimis_g0 wrote:

Is there a database or tool to search for specific transcription factor binding positions on DHS sites?

 

forum genome • 1.5k views
ADD COMMENTlink modified 3.1 years ago by jin80 • written 5.4 years ago by efthimis_g0

thank you for replies that helped a lot

ADD REPLYlink written 5.4 years ago by efthimis_g0
1
gravatar for Alex Reynolds
5.4 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

FIMO is a tool that searches for binding sites in sequences of interest (your DHS sites), for TFs of interest (your TF databases).

ADD COMMENTlink written 5.4 years ago by Alex Reynolds29k
1
gravatar for Kamil
4.4 years ago by
Kamil2.0k
Boston
Kamil2.0k wrote:

You might be interested to read my tutorial on how to use CENTIPEDE to determine if a transcription factor is bound to a genomic site by making use of DNase-Seq data.

ADD COMMENTlink written 4.4 years ago by Kamil2.0k
0
gravatar for vaskin90
5.4 years ago by
vaskin90290
Milan, Italy
vaskin90290 wrote:

With UGENE you can also find TFBSs in your sequences in a single-sequence or in streaming mode. Two methods are available: Weight matrix and SITECON

ADD COMMENTlink written 5.4 years ago by vaskin90290
0
gravatar for jin
3.1 years ago by
jin80
jin80 wrote:

You can try PlantRegMap for TFBS of Plants.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by jin80
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