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I have a list binding site motif of SP1 transcription factor which collects from PWMScan tools. Actually this tool scan whole human genome and give the entire binding motif list. From that list of binding motif I want to align with human genome so that I can find the corresponding gene name.

If any body prescribe the suitable tools name or it will require for any programming.

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  • $\begingroup$ Welcome to the site. Could you please tell us if you know the position of the genome of those binding motifs? Or in which format do you have that list of binding motifs? $\endgroup$ – llrs Sep 4 '18 at 9:11
  • $\begingroup$ Can you post the first few lines of your list so that we know what format it is in? Do you want to find gene promoters that contain this motif? $\endgroup$ – Jared Andrews Sep 4 '18 at 21:50
  • $\begingroup$ yes ....I am giving you two line of the format.. chr1 875622 875633 GCCCCTCCCCC 1676 - MA0079.3 P-value=8.34e-08 chr1 877443 877454 GCCCCTCCCCC 1676 - MA0079.3 P-value=8.34e-08 $\endgroup$ – nayan de Sep 5 '18 at 10:32
  • $\begingroup$ yes ....I am giving you one line of the format.. chr1 875622 875633 GCCCCTCCCCC 1676 - MA0079.3 P-value=8.34e-08 this is for chr 1 start site end site the sequence ....then P value......... Yes I find the gene promoter that contain this motif. If you kindly recomend me tools name then it is very help ful for me.I found this binding motif usning PWMScan tool(ccg.vital-it.ch/pwmtools/pwmscan.php) $\endgroup$ – nayan de Sep 5 '18 at 10:41
  • $\begingroup$ In BED format the list of binding motifs@LIopis $\endgroup$ – nayan de Sep 5 '18 at 10:45

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