Groups
Conversations
All groups and messages
Send feedback to Google
Help
Sign in
Groups
JASPAR Q&A Forum
Conversations
About
JASPAR Q&A Forum
1–30 of 72
Hello!
Welcome to the
JASPAR
Q&A forum.
The latest version of JASPAR is available at
http://jaspar.genereg.net
Best,
Team JASPAR
Mark all as read
Report abusive group
0 selected
Aleksandra Kurowska
,
Anthony Mathelier
2
Mar 29
TFBS download
Dear Aleksandra, Thanks for your interest in JASPAR. The 274 profiles you are referring to were
unread,
TFBS download
Dear Aleksandra, Thanks for your interest in JASPAR. The 274 profiles you are referring to were
Mar 29
Laura Ponting
,
Anthony Mathelier
2
Mar 1
Splice collection removal
Dear Laura, Thanks for your enquiry. In the latest JASPAR release, we discarded unused collections
unread,
Splice collection removal
Dear Laura, Thanks for your enquiry. In the latest JASPAR release, we discarded unused collections
Mar 1
hanwen yu
,
Anthony Mathelier
2
Feb 21
Generate my own JASPAR SQLite file
Dear Hanwen, We currently do not provide this functionality. I guess you should add your motifs
unread,
Generate my own JASPAR SQLite file
Dear Hanwen, We currently do not provide this functionality. I guess you should add your motifs
Feb 21
Brendan Rooney
,
Anthony Mathelier
2
Feb 20
Confirming how to identify putative TF binding sites
Hi Brendan, Yes, you are correct. I would suggest that you use our set of predefined TFBSs provided
unread,
Confirming how to identify putative TF binding sites
Hi Brendan, Yes, you are correct. I would suggest that you use our set of predefined TFBSs provided
Feb 20
Nguyen Xuan-Thang
,
Anthony Mathelier
2
Feb 16
List of TFs gene name and protein name
Hi Thang, Thanks for your interest in JASPAR. The TF gene names are provided in the metadata, which
unread,
List of TFs gene name and protein name
Hi Thang, Thanks for your interest in JASPAR. The TF gene names are provided in the metadata, which
Feb 16
Muhammad Danial
,
Anthony Mathelier
2
11/18/22
How to Download PWM of Ctcf
Click on one of the IDs (they point to the links I gave you in another thread) and then you can
unread,
How to Download PWM of Ctcf
Click on one of the IDs (they point to the links I gave you in another thread) and then you can
11/18/22
Rosanna Di Tinco
, …
Anthony Mathelier
4
11/17/22
How to find TFs starting from promoter region
As I wrote above, you can download the BED files to look for overlap in your region of interest. We
unread,
How to find TFs starting from promoter region
As I wrote above, you can download the BED files to look for overlap in your region of interest. We
11/17/22
Cassandre Coles
, …
Anthony Mathelier
8
11/17/22
Re: Is there any way to display the highest possible score and relative score for a TFBS
Hi Danial, We have 3 PFMs from CTCF: https://jaspar.genereg.net/matrix/MA0139.1/, https://jaspar.
unread,
Re: Is there any way to display the highest possible score and relative score for a TFBS
Hi Danial, We have 3 PFMs from CTCF: https://jaspar.genereg.net/matrix/MA0139.1/, https://jaspar.
11/17/22
dcamer...@gmail.com
,
Anthony Mathelier
3
11/7/22
Jaspar Enrichment missing allEnrichment.tsv output
Hi Anthony, I apologize for the delayed response. I am attempting to restart the process from the
unread,
Jaspar Enrichment missing allEnrichment.tsv output
Hi Anthony, I apologize for the delayed response. I am attempting to restart the process from the
11/7/22
Jessica McAnulty
,
Oriol Fornés
5
9/22/22
Profile Interference Tool
Hi Jessica, I have to update the documentation on GitHub, but I have implemented what you requested.
unread,
Profile Interference Tool
Hi Jessica, I have to update the documentation on GitHub, but I have implemented what you requested.
9/22/22
Malcolm Cook
,
Anthony Mathelier
2
9/5/22
Incorrect link: Cluster-wise Motif Files
Thanks so much for pointing that out. We will fix that asap. Best AM On Wednesday, August 31, 2022 at
unread,
Incorrect link: Cluster-wise Motif Files
Thanks so much for pointing that out. We will fix that asap. Best AM On Wednesday, August 31, 2022 at
9/5/22
Malcolm Cook
,
Anthony Mathelier
3
9/5/22
mal-formed RSAT matrix clusters for JASPAR 2022 Invertebrates !?! (NOT)
Thanks very much for pointing that you. We'll address this as you suggest to make it clearer. On
unread,
mal-formed RSAT matrix clusters for JASPAR 2022 Invertebrates !?! (NOT)
Thanks very much for pointing that you. We'll address this as you suggest to make it clearer. On
9/5/22
Effie Klimi
,
Anthony Mathelier
2
8/30/22
jaspar enrichment analysis - xargs error
Hi Effie, Thanks for your request. It seems the OSX xargs does not allow for long options (see https:
unread,
jaspar enrichment analysis - xargs error
Hi Effie, Thanks for your request. It seems the OSX xargs does not allow for long options (see https:
8/30/22
Malcolm Cook
,
Anthony Mathelier
2
8/26/22
cannot verify jaspar2022.genereg.net's certificate, issued by ‘/C=US/O=Let's Encrypt/CN=R3’:
Thanks very much for the info. Best AM On Friday, August 19, 2022 at 9:29:31 PM UTC+2 malcol...@gmail
unread,
cannot verify jaspar2022.genereg.net's certificate, issued by ‘/C=US/O=Let's Encrypt/CN=R3’:
Thanks very much for the info. Best AM On Friday, August 19, 2022 at 9:29:31 PM UTC+2 malcol...@gmail
8/26/22
Malcolm Cook
,
Anthony Mathelier
2
8/26/22
mysql now sqlite3
Dear Malcolm, Thanks for your interest in JASPAR. We have moved our local instance to sqlite for
unread,
mysql now sqlite3
Dear Malcolm, Thanks for your interest in JASPAR. We have moved our local instance to sqlite for
8/26/22
Malcolm Cook
,
Oriol Fornés
3
8/11/22
sox3 motif changes unrecorded ??
Indeed - thanks for the correction and tip. On Thursday, August 11, 2022 at 4:14:06 PM UTC-5 oriol...
unread,
sox3 motif changes unrecorded ??
Indeed - thanks for the correction and tip. On Thursday, August 11, 2022 at 4:14:06 PM UTC-5 oriol...
8/11/22
Sharon Torigoe
,
Anthony Mathelier
2
6/6/22
Using JASPAR for publications
Hi Sharon, Of course, that's no problem at all as long as the JASPAR paper is appropriately cited
unread,
Using JASPAR for publications
Hi Sharon, Of course, that's no problem at all as long as the JASPAR paper is appropriately cited
6/6/22
Peter Cockerill
,
anthony....@gmail.com
2
5/31/22
motif MA1621.1 binds to Ptf1a and not to Rbpj or Rbpjl. You need to relabel this motif as Ptf1a.
Thank you very much for raising this issue. I agree with you and we will fix this issue asap. On
unread,
motif MA1621.1 binds to Ptf1a and not to Rbpj or Rbpjl. You need to relabel this motif as Ptf1a.
Thank you very much for raising this issue. I agree with you and we will fix this issue asap. On
5/31/22
Selam Solomon
,
anthony....@gmail.com
2
5/5/22
TF protein sequences
Dear Selam, We do not provide that unfortunately. On Friday, April 29, 2022 at 10:50:25 AM UTC+2
unread,
TF protein sequences
Dear Selam, We do not provide that unfortunately. On Friday, April 29, 2022 at 10:50:25 AM UTC+2
5/5/22
Laura Farr
, …
anthony....@gmail.com
4
5/5/22
"Familial profile #" in UCSC browser
Dear Wojciech, You have a good point here. We provide the mapping but in a non-parsable way, which is
unread,
"Familial profile #" in UCSC browser
Dear Wojciech, You have a good point here. We provide the mapping but in a non-parsable way, which is
5/5/22
Nusrat Hossain
,
anthony....@gmail.com
2
4/28/22
webpage loading issue
Sorry for the delayed reply. I assume it has been fixed now. On Tuesday, July 27, 2021 at 6:30:20 PM
unread,
webpage loading issue
Sorry for the delayed reply. I assume it has been fixed now. On Tuesday, July 27, 2021 at 6:30:20 PM
4/28/22
Orsolya Liska
,
anthony....@gmail.com
2
4/28/22
assembly versions of TF binding sites
Unfortunately, these BED files were created too long ago and the assembly version was not recorded
unread,
assembly versions of TF binding sites
Unfortunately, these BED files were created too long ago and the assembly version was not recorded
4/28/22
Tania Cid
,
anthony....@gmail.com
2
4/28/22
Negative score
Hi Tania, The score corresponds to the PWM score, which is the sum of positive and negative scores in
unread,
Negative score
Hi Tania, The score corresponds to the PWM score, which is the sum of positive and negative scores in
4/28/22
Farzin Mohamadi
, …
anthony....@gmail.com
3
4/28/22
Frequency matrix 'G' and 'T' rows in reverse compliment remain the same
Sorry for the delay in addressing this Farzin. This has now been fixed. Thanks for raising the issue.
unread,
Frequency matrix 'G' and 'T' rows in reverse compliment remain the same
Sorry for the delay in addressing this Farzin. This has now been fixed. Thanks for raising the issue.
4/28/22
Cash Kumar
,
anthony....@gmail.com
2
4/28/22
TFs
I suggest that you look at the JASPAR and UniBind TFBS predictions and intersect them with your
unread,
TFs
I suggest that you look at the JASPAR and UniBind TFBS predictions and intersect them with your
4/28/22
Aki Hoji
, …
田文浩
6
4/19/22
save output of scan
Afraid not. If you need help for using this extension you can contact me at 12509...@qq.com. I can
unread,
save output of scan
Afraid not. If you need help for using this extension you can contact me at 12509...@qq.com. I can
4/19/22
Rafael Soler Ortuño
, …
Rafael Soler Ortuño
3
12/17/21
Add a new TF
Thank you so much Jaime! :) El dia dijous, 16 de desembre de 2021 a les 11:33:52 UTC+1, loka...@gmail
unread,
Add a new TF
Thank you so much Jaime! :) El dia dijous, 16 de desembre de 2021 a les 11:33:52 UTC+1, loka...@gmail
12/17/21
Xiuru Dai
,
Anthony Mathelier
2
12/13/21
Profile summary for JASPAR plant motif
Dear Xiuru, You could use our new pyJASPAR package to get this (https://pypi.org/project/pyjaspar/).
unread,
Profile summary for JASPAR plant motif
Dear Xiuru, You could use our new pyJASPAR package to get this (https://pypi.org/project/pyjaspar/).
12/13/21
lei gu
, …
Anthony Mathelier
3
12/8/21
3000 nucleotides limitation
You could also use the JASPAR Biopython package or the very fast PWMscan tool (https://academic.oup.
unread,
3000 nucleotides limitation
You could also use the JASPAR Biopython package or the very fast PWMscan tool (https://academic.oup.
12/8/21
hui xiao
, …
loka...@gmail.com
4
11/17/21
species selection issue
Hi Nathan Thanks for let us know about this issue. We are currently working on it (and in other bugs/
unread,
species selection issue
Hi Nathan Thanks for let us know about this issue. We are currently working on it (and in other bugs/
11/17/21