HOCOMOCO V12 in PWMScan

[Anja Estermann]

Dear PWMScan developers,

I just found out about the PWMScan tool. It is exactly what I was looking for, as other websites only provide predictions for shorter DNA sequences and not whole genome. I noticed, that the newest version of HOCOMOCO V12 is not available. Is it in planning to be added?

So far, I was using the searchSeq function of the TFBSTools in R for prediction of TFBS. I noticed, that this is not a commonly used method. Do you know whether it would be preferable to use another method?

Thank you and best regards,
Anja

[phbu06]

Dear Anja,

Thanks for reminding us that HOCOMOCO V12 is not yet installed on the PWMScan server. We'll add the new version as soon as possible and confirm via this conversation when it's done.

I haven't use TFBSTools myself. So I cannot give you an opinion as to its suitability.

In the supplementary Material to the PWMScan paper:

htps://academic.oup.com/bioinformatics/article/34/14/2483/4921176#supplementary-data

we presented a comparison of 7 motif scanners (Chapter 2: "Comparison with other motif scanning software", and Supplementary Table 4. "Motif Scanning Software Comparison"

There, you may find useful information for choosing the software tool which best suits your needs.

Philipp

[phbu06]

Dear Anja,

Sorry, this has taken a long time.

The HOCOMOCOv12 CORE (HUMAN + MOUSE orthologs) TF Collection is now installed at the back end of the PWMTools server 

at https://epd.expasy.org/pwmtools/. I hope it will still be useful to you. If you note any problems or irregularities, please report via this mailing list. 

 Philipp