## Installing external software

Chipster relies on external programs for promoter analysis. ClusterBuster is needed for searching the known transcription factor binding sites, and Weeder is used for inferring the common elements in the promoter sequences, i.e., finding possible unknown transcription factor binding sites.

Chipster also depends on external programs for multiple sequence alignment and phylogenetic analysis. Muscle and Mafft are used for sequence alignment, seqret from the EMBOSS package for sequence format conversion and RAxML and ClustalW for phylogenetic analysis.

### R and Bioconductor

- Install R 2.6.1 from http://www.r-project.org.
- Run the installation script in R (you should have writing permissions to the install folder).
- Download and install the packages fpc (v. 1.1-5) and A2R (v. 0.04) from http://addictedtor.free.fr/packages/
- Download and install Affymetrix exon array CDFs from http://xmap.picr.man.ac.uk/download/index.jsp#2
- In addition you will need to install Illumina Probe ID annotation packages. Those should be available from http://www.bioconductor.org/packages/2.2/data/annotation/

### ClusterBuster and Weeder

#### Installing executables

Download and install ClusterBuster (v. ?.?.?) and Weeder (v. 1.3). These can be downloaded from:

http://cagt.bu.edu/page/ClusterBuster_download

http://www.pesolelab.it/index.php?mod=04_Tools

In the R scripts promoter-cbust.R and promoter-tfbs.R change the paths to the executable to be correct.

Weeder needs to be able to link to frequency files, and the location of these is indicated in the promoter-tfbs.R script. These need to be changed to point to a correct location, also.

#### Installing matrix files

Download the Jaspar database for ClusterBuster from:

http://zlab.bu.edu/clover/jaspar2

Rename the file as jaspar2005core.txt, and modify the path to it in the script promoter-cbust.R.

#### Installing promoter sequence files

Promoter analysis tools need the promoter sequences in a suitable format. Download the promoter sequence file for human, mouse and rat from http://hgdownload.cse.ucsc.edu/downloads.html, and for yeast from http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/Cell_cycle_data/upstream_seq.html.

Run the accessory script promoter-accessory.R for these sequence files. The result is a bunch of tabular files that can be easily handled with R. The path to these files needs to be changed in the scripts promoter-cbust.R, promoter-tfbs.R and promoter-retrprom.R.

### Sequence analysis and phylogenetics tools

Download and install the following programs:

Mafft v. 6.240

Muscle v. 3.6

EMBOSS v. 5.0.0

ClustalW v. 2.0.4

RAxML HPC v. 7.0.0

The script seqanal-msa.R and seqanal-phylogenetics.R contain paths to these executables. Please modify the path according to your system.