You may download and install your own local copy of CAGEd-oPOSSUM.
Please see the INSTALL file included in the top-level of the CAGEd-oPOSSUM source code for details on how to perform a local installation.
Download the full CAGEd-oPOSSUM source code including the API, stand-alone analysis scripts and web code directly from the web page here: CAGEd_oPOSSUM.tar.gz
The CAGEd-oPOSSUM source code is also available as a public repository on GitHub at: https://github.com/wassermanlab/CAGEd-oPOSSUM.
There are two CAGEd-oPOSSUM databases of pre-computed transcription factor binding sites, one for each species:
As well there is our local copy of the JASPAR database of transcription factor binding site profiles:
By far the preferred way to download these databases is via our FTP site as CAGEd-oPOSSUM human and mouse databases are quite large (tens of Gigabytes).
The two CAGEd-oPOSSUM species database are located in the
CAGEd_oPOSSUM/databases sub-directory and the JASPAR database is located in the
As the JASPAR database is quite small you may also download it directly from the database server using the mysldump facility.
NOTE: It is necessary to use the --skip-lock-tables option when using mysqldump.
The JASPAR_2016 database is hosted on our vm5.cmmt.ubc.ca server and may be downloaded using the MySQL user jaspar_r:
$ mysqldump -h vm5.cmmt.ubc.ca -u jaspar_r --skip-lock-tables JASPAR_2016 > JASPAR_2016.sql
As the CAGEd-oPOSSUM human and mouse databases are quite large please download them from our FTP server. If for some reason you are unable to download them via FTP please email us a 'opossum AT cmmt DOT ubc DOT ca' and we will try to rectify the problem or grant you permission to directly mysqldump them from our servers.