cpgreport

cpgreport

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cpgreport scans a nucleotide sequence for regions with higher than expected frequencies of the dinucleotide CG.

Here is a sample session with cpgreport:

% cpgreport embl:rnu68037 Reports CpG rich regions CpG score [17]: Output file [rnu68037.cpgreport]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

-score (integer)

This sets the score for each CG sequence found. A value of 17 is more sensitive, but 28 has also been used with some success.

[-outfile] (outfile)

Output filename.

Advanced qualifiers:

-featout (featout)

File for output features.