Clover (DISABLED - will be removed on 12/22/17)
Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/22/17. If you need this software, please contact email@example.com.
Clover is a program for identifying functional sites in DNA sequences. For a set of DNA sequences that share a common function, it will compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which if any of the motifs are statistically overrepresented in the sequence set.
To run this software in a Linux environment run the commands:
module load clover
Clover requires two input files: one containing DNA sequencesin FASTA format and the other sequence motifs. Several options for sequence motifs exist. One is JASPAR
, a database of transcription factor binding site patterns. A commercial database, TRANSFAC
, is also available. More information on using these database, including converting formats, is available on the Clover homepage.
An example of running clover is given below:
clover -t 0.05 mymotifs myseqs.fa background1.fa background2.fa
To view available options for Clover, use the following command:
Further documentation may be found at the Clover homepage.