EMBOSS: compseq

| ## EMBOSS: compseq

# Program compseq

## Function

Counts the composition of dimer/trimer/etc words in a sequence

## Description

This takes a specified length of sequence and counts the number of distinct subsequences of that length that there are in the input sequence(s). It can read in the result of a previous compseq analysis and use this to set the expected frequencies of the subsequences.

## Usage

Here is a sample session with compseq.

    To count the frequencies of dinucleotides in a file:

    % compseq  embl:hsfau  2  result3.comp

    To count the frequencies of hexanucleotides, without outputting
    the results of hexanucleotides that do not occur in the sequence:

    % compseq  embl:hsfau  6  result6.comp  -nozero

    To count the frequencies of trinucleotides in frame 2 of a sequence
    and use a previously prepared compseq output to show the expected
    frequencies:

    % compseq  embl:hsfau  3  result3.comp  -frame 2  -in prev.comp

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-word]              integer    This is the size of word (n-mer) to count.
                                      Thus if you want to count codon frequencies,
                                      you should enter 3 here.
      [-outfile]           outfile    This is the results file.

       Optional qualifiers (* if not always prompted):
       -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 and analysing a
                                      nucleotide sequence.
       -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.
    *  -[no]ignorebz       bool       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.
    *  -reverse            bool       Set this to be true if you also wish to also
                                      count words in the reverse complement of a
                                      nucleic sequence.
       -[no]zerocount      bool       You can make the output results file much
                                      smaller if you do not display the words with
                                      a zero count.

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-word] (Parameter 2) | This is the size of word (n-mer) to count. Thus if you want to count codon frequencies, you should enter 3 here. | Integer from 1 to 20 | 2
[-outfile] (Parameter 3) | This is the results file. | Output file | <sequence>.compseq
Optional qualifiers | Allowed values | Default
-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 and analysing a nucleotide sequence. | Input file | Required
-frame | 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. | Integer 0 or more | 0
-[no]ignorebz | 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 | Yes
-reverse | Set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence. | Yes/No | No
-[no]zerocount | You can make the output results file much smaller if you do not display the words with a zero count. | Yes/No | Yes
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Normal sequence(s) USA.

## Output file format

The output format consists of:

Header information and comments are preceeded by a '#' character at the start of the line.

The Word size and the Total count are then given on separate lines,

The headers of the columns of results are preceeded by a '#'

The results columns are: the sub-sequence word, the observed frequency, the expected frequency (which will be read from the input file if one is given, else it is a simple inverse of the number of words of the size specified that can be constructed), the ratio of the observed to expected frequency.

After a blank line at the end, the results of 'Other' words is given - this is the number of words with a sequence which has IUPAC ambiguity codes or other unusual characters in.

Example:

    #
    # Output from 'compseq'
    #
    # The Expected frequencies are taken from the file: jjj.composition
    #
    # The input sequences are:
    #       jjj

    Word size       2
    Total count     196

    #
    # Word  Obs Count       Obs Frequency   Exp Frequency   Obs/Exp Frequency
    #
    AA      0               0.0000000       0.0000000       10000000000.0000000
    AC      18              0.0918367       0.0918367       1.0000004
    AG      8               0.0408163       0.0408163       1.0000007
    AT      12              0.0612245       0.0612245       0.9999998
    CA      3               0.0153061       0.0153061       1.0000015
    CC      1               0.0051020       0.0051020       1.0000080
    CG      16              0.0816327       0.0816327       0.9999994
    CT      15              0.0765306       0.0765306       1.0000002
    GA      16              0.0816327       0.0816327       0.9999994
    GC      13              0.0663265       0.0663265       1.0000005
    GG      5               0.0255102       0.0255102       1.0000002
    GT      18              0.0918367       0.0918367       1.0000004
    TA      19              0.0969388       0.0969388       0.9999997
    TC      4               0.0204082       0.0204082       0.9999982
    TG      22              0.1122449       0.1122449       1.0000000
    TT      5               0.0255102       0.0255102       1.0000002

    Other   21              0.0255102       0.1071429       0.2380951

## Data files

The input data file is not required.

The input data file format is exactly the same as the output file format.

It expects to read in a previous output file of this program. An error is produced if the word size of the current compseq job and that of the output file being read in are different.

## Notes

The results are held in an array in memory before being written to a file. For large values of wordsize, you may run out of memory.

You can produce very large output files if you choose large values of wordsize.

## References

None.

## Warnings

If you use large word-sizes (over about 7 for nucleic, 5 for protein) you will use huge amounts of memory.

## Diagnostic Error Messages

"The word size is too large for the data structure available."
  You chose a word size that cannot be stored by the program.
"Insufficient memory - aborting."
  You do not have enough memory - use a machine with more memory.
"The word size you are counting (n) is different to the word size in the file of expected frequencies (n)."
  You chose different word sizes in the run of compseq that produced your results file used to display the expected word frequencies to the word size used in this run of compseq.
"The 'Word size' line was not found, instead found:"
  You appear to be trying to read a corrupted compseq results file

## Exit status

It always exits with status 0 unless one of the above error conditions is found

## Known bugs

This program can use a large amount of memory is you specify a large word size (7 or above). This may impact the behaviour of other programs on your machine.

If you run out of memory, you may see the program crash with a generic error message that will be specific to your machine's operating system, but will probably be a warning about writing to memory that the program does not own (eg "Segmentation fault" on a Solaris machine)

This is not a bug, it is a feature of the way this program grabs large amounts of memory.

## See also

Program name | Description
--- | ---
backtranseq | Back translate a protein sequence
banana | Bending and curvature plot in B-DNA
btwisted | Calculates the twisting in a B-DNA sequence
chaos | Create a chaos game representation plot for a sequence
charge | Protein charge plot
checktrans | Reports STOP codons and ORF statistics of a protein sequence
dan | Calculates DNA RNA/DNA melting temperature
emowse | Protein identification by mass spectrometry
freak | Residue/base frequency table or plot
iep | Calculates the isoelectric point of a protein
isochore | Plots isochores in large DNA sequences
mwfilter | Filter noisy molwts from mass spec output
octanol | Displays protein hydropathy
pepinfo | Plots simple amino acid properties in parallel
pepstats | Protein statistics
pepwindow | Displays protein hydropathy
pepwindowall | Displays protein hydropathy of a set of sequences
wordcount | Counts words of a specified size in a DNA sequence

## Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

Completed 2 March 2000
5 April 2001 (version 1.12.0) - the operation of the option '-reverse' has changed. It is now 'False' by default instead of being 'True' by default for nucleic sequences. Too many people were getting confused by the counts being done on both senses, so this is now done on only the forward sense by default.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments