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compseq - Calculate the composition of unique words in sequences


compseq -sequence seqall [-infile infile] -word integer [-frame integer] -ignorebz boolean
-reverse boolean [-calcfreq boolean] -outfile outfile [-zerocount boolean]

compseq -help


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


Input section
-sequence seqall

-infile infile
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.

Required section
-word integer
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

Additional section
-frame integer
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.

-ignorebz boolean
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

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

-calcfreq boolean
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

Output section
-outfile outfile
This is the results file.

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

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