4/24/2002 : added -z option
Download Cister binary for Linux (Debian 10.6)
Don't forget to make the file executable by using chmod +x
cister -i myseqs.fa -m mymatrices -a 20 -b 8 -g 30000 -c clusterout -o motifout
>first_sequence AGGTCGAG... GTGGAAC... >second_sequence ...
Use this option to supply the program with a file containing a list of nucleotide count matrices. Each matrix defines the DNA sequence motif of a cis-element. The file has the following format:
>first_motif 1 1 5 2 38 5 29 1 15 5 3 7 5 35 >second_motif 1 1 4 2 2 12 ...The first line of each matrix definition begins with the symbol > followed by a name for the motif. The second line, which is optional, specifies two weights for the motif: one for the + strand and the other for the - strand. These weights let you specify how often you expect each cis-element to occur on each strand in regulatory clusters. The weights are relative, so multiplying all the weights for all the motifs by a constant makes no difference. If in doubt, leave it out. The remaining lines contain counts of adenine, cytosine, guanine and thymine observed at each position in the cis-element, in a sample of cis-elements of this type.
Palindromes: for matrices that are exact complementary palindromes, there is no distinction between the + and - strand. Cister automatically detects exact complement palindromes, and assigns an overall weight for the motif that is the sum of the two numbers on the second line of the matrix description.