<p>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. </p>

<p>If any body prescribe the suitable tools name or it will require for any programming.</p>

CC BY-SA 4.0
2018-09-04T09:11:32.073Z
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?
llrs
CC BY-SA 4.0
2018-09-04T21:50:27.363Z
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?
Jared Andrews
CC BY-SA 4.0
2018-09-05T10:32:15.770Z
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
nayan de
CC BY-SA 4.0
2018-09-05T10:41:13.223Z
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(https://ccg.vital-it.ch/pwmtools/pwmscan.php)
nayan de
CC BY-SA 4.0
2018-09-05T10:45:30.160Z
In BED format  the list of binding motifs@LIopis
nayan de
<gene><genome><transcriptome><motifs>
Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix
# Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix

(Asked by: username_0 on 2018-09-04)

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.

**Tags:** gene, genome, transcriptome, motifs
> **Comments:**
> **username_1**: 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?  
> **username_2**: 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?  
> **username_0**: 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  
> **username_0**: 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(https://ccg.vital-it.ch/pwmtools/pwmscan.php)  
> **username_0**: In BED format  the list of binding motifs@LIopis  

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## 0 answers

