
This folder contains the actual program (‘CiiiDER.jar') and some supplementary files.

The 'Matrices' folder contains two publicly available transcription factor model libraries: the JASPAR core non-redundant vertebrate matrices (Sandelin NAR 2004; Khan NAR 2018) and matrices from a large SELEX experimental dataset (Jolma et al 2012 Cell). 
To access these easily from CiiiDER, place the ‘Matrices' folder in the same directory as ‘CiiiDER.jar’ (see attached picture). If you have any other transcription factor model files, such the TRANSFAC vertebrate matrices, you can place these in this ‘Matrices' folder too. The JASPAR matrices are a good place to start.

The ‘Genomes’ folder contains a subfolder with an appropriate FASTA file and a GTF file. These are not necessary if you want to scan FASTA-format sequences for transcription factor binding sites, but these will allow you to enter lists of genes or ENSEMBL IDs instead of finding promoter sequences yourself. A GLM file will be created the first time you use the program, which will increase the speed of subsequent analyses.

There are also some instructions (CiiiDER Documentation Draft.docx) available, which may be helpful.


Please email us (bioinformatics.ciiid-l@hudson.org.au) if you have any questions.