The Jaspar subsequence files were generated from the JASPAR_CORE 2009, All_Species redundant set of profiles. From the Jaspar website: "The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc) consist of the open data acess, non-redundancy and quality. 
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount."

The original files were downloaded from the Jaspar site.

http://jaspar.cgb.ki.se/

The profiles were converted to subsequences, and then manually curated.

Please note that profile scanning is more sensitive than subsequence file scanning.  If you are looking for a particular transcription factor then you are recommended to the Nucleic Acid Toolbox and use one of the JASPAR2009 profiles directly.  The JASPAR ID is in the description of each subsequence in the subsequence file.


4 March 2010