Find protein sequence regions with a biased composition emboss oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto Sequences This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words Yes No You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html