compseq - Calculate the composition of unique words in sequences

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EMBOSS 6.4.0                                       05/11/2012                                        COMPSEQ(1e)

compseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It
       is part of the "Nucleic:Composition,Protein:Composition" command group(s).

       compseq - Calculate the composition of unique words in sequences

Inputsection-sequenceseqall-infileinfile
           This is a file previously produced by 'compseq' that can be used to set the expected frequencies of
           words in this analysis. The word size in the current run must be the same as the one in this results
           file. Obviously, you should use a file produced from protein sequences if you are counting protein
           sequence word frequencies, and you must use one made from nucleotide frequencies if you are analysing
           a nucleotide sequence.

   Requiredsection-wordinteger
           This is the size of word (n-mer) to count. Thus if you want to count codon frequencies for a
           nucleotide sequence, you should enter 3 here. Default value: 2

   Additionalsection-frameinteger
           The normal behaviour of 'compseq' is to count the frequencies of all words that occur by moving a
           window of length 'word' up by one each time. This option allows you to move the window up by the
           length of the word each time, skipping over the intervening words. You can count only those words
           that occur in a single frame of the word by setting this value to a number other than zero. If you
           set it to 1 it will only count the words in frame 1, 2 will only count the words in frame 2 and so
           on.

       -ignorebzboolean
           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. Default value: Y

       -reverseboolean
           Set this to be true if you also wish to also count words in the reverse complement of a nucleic
           sequence. Default value: N

       -calcfreqboolean
           If this is set true then the expected frequencies of words are calculated from the observed frequency
           of single bases or residues in the sequences. If you are reporting a word size of 1 (single bases or
           residues) then there is no point in using this option because the calculated expected frequency will
           be equal to the observed frequency. Calculating the expected frequencies like this will give an
           approximation of the expected frequencies that you might get by using an input file of frequencies
           produced by a previous run of this program. If an input file of expected word frequencies has been
           specified then the values from that file will be used instead of this calculation of expected
           frequency from the sequence, even if 'calcfreq' is set to be true. Default value: N

   Outputsection-outfileoutfile
           This is the results file.

       -zerocountboolean
           You can make the output results file much smaller if you do not display the words with a zero count.
           Default value: Y

       compseq is fully documented via the tfm(1) system.

compseq-sequenceseqall [-infileinfile] -wordinteger [-frameinteger] -ignorebzboolean-reverseboolean [-calcfreqboolean] -outfileoutfile [-zerocountboolean]

       compseq-help