Bioconductor Package MotifDb: LICENSE MotifDb is a collection of position weight matrices and metadata obtained from six sources, with some restriction upon commercial use as described below: | 2769 position frequency matrices from 6 sources: | FlyFactorSurvey: 614 | JASPAR_CORE: 459 | ScerTF: 196 | UniPROBE: 380 | hPDI: 437 | stamlab: 683 FlyFactorSurvey: all data described as "public" [http://pgfe.umassmed.edu/ffs/DownloadData.php] JASPAR_CORE: "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." [http://jaspar.genereg.net/] ScerTF: "The entire database of optimal matrices selected for all S. cerevisiae transcription factors is available for download here." No restrictions mentioned. Spivak and Stormo explain that they curated their collection from ten sources, listed here: http://stormo.wustl.edu/ScerTF/download/. UniPROBE: "Please note that any files which contain PBM probe sequences are protected by an academic research use license, which will require confirmation prior to file download." (from ). I exchanged email with Martha Bulyk and her staff in May 2012, explained the MotifDb project, they were helpful. I will check my import code to see whether I use their PBM probe sequences. hPDI: "The content in the hPDI database is free to academic and non-profit organizations. Users for commercial purpose please contact the authors before download the data sets." stamlab: These motifs are part of the ENCODE project, and (I assume) public.