Obtaining PFMs

[Dinithi Wanniarachchi]

Hello,

is it okay if I use older versions of binding sites (eg:MA0556.1,MA0003.2) instead of the latest ones since the older versions have flanking sequences as well and I need them?.

Also I would like to know whether the binding sites available in both JASPAR and Unibind is same. For an example AP3(MA00556.1) is available in both JASPAR and Unibind but I feel the binding sites are different. If so, can you tell me the reason?.

Your response will be very helpful.

Thank you in advance.

[Anthony Mathelier]

You can use the version you want but we would still recommend to use the latest version of the profiles.

The binding sites in JASPAR and UniBind are different. The binding sites in JASPAR are the ones used to create the PFM while the ones in UniBind are derived from ChIP-seq experiments using our ChIP-eat pipeline (see https://doi.org/10.1186/s12864-021-07760-6).