Download Comet binary for Linux (Redhat 7.1)
Download Comet binary for Alpha (Compaq Tru64 UNIX V5.0A)
Download Comet binary for Sun (Solaris 8)
Download Comet binary for SGI / IRIX
Download Comet binary for Mac OS X (thanks to Eric Frangulian)
Don't forget to make the file executable by using chmod +x
Example usage:
comet -i myseqs.fa -m mymatrices -a 20 -o outfile
Options
>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. Comet 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.
The E-values will not be accurate when using a collection of cis-element matrices including: very similar matrices, a matrix that is almost a complementary palindrome, or a matrix with a high propensity for self-overlap, e.g. consensus sequence AAAAAA. It is recommended that very similar matrices be combined into a single matrix, and near-palindromic matrices be made exactly palindromic.