how to find motif by UCSC

Question

[newbiebio]

I have several transcript factor and want to exact their motif by UCSC. The result should have motif position, motif probablity and motif sequence.

Answer 1

[Alex Reynolds]

If you have the TF probability model, you can do a FIMO scan to get the position, probability and sequence.

Answer 2

[genecats.ucsc]

Hello.

Thank you for your question about finding transcription factor binding motifs in the UCSC Genome Browser. We have several tracks for the human hg19 assembly that include transcription factor binding information:

• ENCODE Transcription Factor Binding: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeTfBindingSuper
• HMR Conserved Transcription Factor Binding Sites: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=tfbsConsSites
• Transcription Factor ChIP-seq (161 factors) from ENCODE with Factorbook Motifs: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3

You can also search our public mailing list archives to see other questions related to transcription factor binding motifs: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/transcription$20factor$20motif%7Csort:date.

If you have any follow-up questions, it would be helpful if you could post them to our Google Groups forum: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome, that way our whole team can see the question and help with an answer.

Thanks,

Matthew from the UCSC Genome Browser

Answer 3

[samzhao]

see this https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/2vPu0t7BDuw