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 group(s).
-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.
-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
-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
-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
Bugs can be reported to the Debian Bug Tracking system
(http://bugs.debian.org/emboss), or directly to the EMBOSS developers
(http://sourceforge.net/tracker/?group_id=93650&atid=605031).
compseq is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
This manual page was autogenerated from an Ajax Control Definition
of the EMBOSS package. It can be redistributed under the same terms as
EMBOSS itself.