COMPSEQ(1e) | EMBOSS Manual for Debian | COMPSEQ(1e) |
NAME¶
compseq - Calculate the composition of unique words in sequencesSYNOPSIS¶
compseq
-sequence seqall
[-infile infile]
-word integer [
-frame integer]
-ignorebz boolean
-reverse boolean [
-calcfreq boolean]
-outfile outfile [
-zerocount boolean]
compseq
-help
DESCRIPTION¶
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).OPTIONS¶
Input section¶
-sequence seqall -infile infileThis 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 integerThis 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 integerThe 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 outfileThis 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¶
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).SEE ALSO¶
compseq is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this
manual page.
COPYRIGHT¶
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.05/11/2012 | EMBOSS 6.4.0 |