Transcription factor binding on DHS sites

Question

[efthimis_g]

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

[efthimis_g]

thank you for replies that helped a lot

Answer 1

[Alex Reynolds]

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

Answer 2

[Kamil]

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.

Answer 3

[vaskin90]

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.

Answer 4

[jin]

You can try PlantRegMap for TFBS of Plants.