
                                  oddcomp 



Function

   Finds protein sequence regions with a biased composition

Description

   oddcomp searches a series of protein files, reporting the identifier
   for those that exceed a certain amino acid composition threshold in a
   portion of the sequence.

   oddcomp was written to answer the question 'which proteins contain at
   least n X and m Y in p residues'.

   One could search for serine rich or polyglutamine rich, collagen
   helix, or similar proteins using this program.

   oddcomp takes as input an amino acid composition data file in the same
   format as the output from compseq. It can tolerate any word length
   within reason for the memory capacity of the machine in question. Only
   the first two fields in the composition data file are used: the word
   and the number of occurrences. Any word not mentioned is initialised
   to a threshold of zero.

   oddcomp measures the amino acid composition (this can be dimers etc as
   well as monomers) in a sliding window. If and when composition meets
   or exceeds all the specified thresholds, the sequence is reported and
   oddcomp moves to the next sequence. It does not report where in the
   sequence it found the matching region, merely the sequence ID.

   oddcomp was originally written to identify SR/RS containing proteins.
   eg. specifying a window of forty amino acids containing at least 3 SR
   and 4 RS words.

   To search for a specific set of words in a sequence, edit the input
   composition data file to delete any words from the input file in which
   you are not interested. The search is a boolean AND so there must be
   (from the short example above) at least 3 SR AND at least 4 RS for the
   sequence to be reported. If your total words specified exceeds
   window-wordlength+1 you will never get any hits.

   Only one word size can be used and is specified at the top of the file
   in compseq-style output.

Usage

   Here is a sample session with oddcomp

   To search for entries in swissprot with at least 1 SR AND at least 2
   RS:


% oddcomp 
Finds protein sequence regions with a biased composition
Input sequence(s): tsw:*
Compseq output file to use for expected word frequencies: oddcomp.comp
Window size to consider (e.g. 30 aa) [30]: 
Output file [100k_rat.oddcomp]: out.odd

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-compdatafile]      infile     This is a file in the format of the output
                                  produced by 'compseq' that is used to set
                                  the minimum frequencies of words in this
                                  analysis.
  [-window]            integer    This is the size of window in which to
                                  count.
                                  Thus if you want to count frequencies in a
                                  40 aa stretch you should enter 40 here.
  [-outfile]           outfile    This is the results file.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -[no]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.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated qualifiers
   -odirectory4         string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-compdatafile]
   (Parameter 2) This is a file in the format of the output produced by
   'compseq' that is used to set the minimum frequencies of words in this
   analysis. Input file Required
   [-window]
   (Parameter 3) This is the size of window in which to count. Thus if
   you want to count frequencies in a 40 aa stretch you should enter 40
   here. Integer 10 or more 30
   [-outfile]
   (Parameter 4) This is the results file. Output file <sequence>.oddcomp
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -[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. Boolean value
   Yes/No Yes

Input file format

  Input files for usage example

   'tsw:*' is a sequence entry in the example protein database 'tsw'

  File: oddcomp.comp

# Example input file for oddcomp
Word size       2
Total count     0

#
# Word  Obs Count       Obs Frequency   Exp Frequency   Obs/Exp Frequency
#
RS      2               0               0               0
SR      1               0               0               0

Other   0               0               0               0

   The columns "Obs Frequency", "Exp Frequency" and "Obs/Exp Frequency"
   are not required - they were simply included in this example to show
   the similarity between this input file format and the output of the
   program compseq. A compseq output file can be used as the input to
   oddcomp - the extra columns are ignored by oddcomp.

   A minimal composition input data file would look like this:
     _________________________________________________________________

Word size       2
Total count     0
RS      2
SR      1
     _________________________________________________________________

   Blank lines and lines starting with '#' are ignored.

   The first non-comment line should start with 'Word size' and will
   specify the word size to use.

   A line starting with the word 'Total' is required.

   Anything after the line starting with the word 'Total' will be read as
   word count data.

   Word count data consists of a word to search for and the count of that
   word to search for within the sliding window. The columns are
   separated by one or more spaces or TAB characters. Anything after
   these two columns will be ignored.

Output file format

   oddcomp writes a list of sequence name identifiers.

  Output files for usage example

  File: out.odd

#
# Output from 'oddcomp'
#
# The Expected frequencies are taken from the file: ../../data/oddcomp.comp
#
#       Word size: 2
        CB1B_FUGRU
        CO9_FUGRU
        FOS_FUGRU
        RS7_FUGRU

#       END     #

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

    Program name                         Description
   antigenic      Finds antigenic sites in proteins
   digest         Protein proteolytic enzyme or reagent cleavage digest
   epestfind      Finds PEST motifs as potential proteolytic cleavage sites
   fuzzpro        Protein pattern search
   fuzztran       Protein pattern search after translation
   helixturnhelix Report nucleic acid binding motifs
   patmatdb       Search a protein sequence with a motif
   patmatmotifs   Search a PROSITE motif database with a protein sequence
   pepcoil        Predicts coiled coil regions
   preg           Regular expression search of a protein sequence
   pscan          Scans proteins using PRINTS
   sigcleave      Reports protein signal cleavage sites

Author(s)

   David Martin (dmartin © rfcgr.mrc.ac.uk)

History

   Written (1999) - David Martin

Target users

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

Comments

   None
