                                   oddcomp



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Function

   Identify proteins with specified sequence word composition

Description

   oddcomp reads one or more protein sequences, identifies proteins
   containing regions with a specific sequence word composition, then
   writes a list of sequence identifiers of those proteins to an output
   file. The word composition is read from an input file which gives the
   minimum word occurence for any number of sequence words. For an input
   sequence to be listed in the output file, each word must be found at
   least the stated number of times in any window over the input sequence.
   The window size may be set to any value or the length of the current
   protein (-fullwindow option).

Algorithm

   The input file of sequence word composition data is in the same format
   as the output from compseq. Only one word size (of any length) can be
   used and is specified at the top of the file. The search for words is a
   boolean AND meaning all words given in the file must be found in a
   sequence for it to be reported.

   Each word must occur at least the stated number of times in a window
   over an input sequence for the sequence to be reported. The word size
   given in the input data file must be less than the specified window
   size; you will not get any hits otherwise.

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
Identify proteins with specified sequence word composition
Input protein sequence(s): tsw:*
Program compseq output file: oddcomp.comp
Window size to consider (e.g. 30 aa) [30]:
Output file [cru4_arath.oddcomp]: out.odd


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

Command line arguments

Identify proteins with specified sequence word composition
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
  [-infile]            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    [30] 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)
  [-outfile]           outfile    [*.oddcomp] This is the results file.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fullwindow         toggle     [N] Set this option on (Y) if you want the
                                  window size to be set to the length of the
                                  current protein. Otherwise, leave this
                                  option unset, in which case you'll be
                                  prompted for a window size to use.
   -[no]ignorebz       boolean    [Y] 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit


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
        CNR1B_TAKRU
        CO9_TAKRU
        FOS_TAKRU
        RS7_TAKRU
        UBR5_RAT

#       END     #

Data files

   None.

Notes

   oddcomp was originally written to identify proteins with SR/RS dimers,
   for example, windows of forty amino acids containing at least 3 SR and
   4 RS words. More generally, it will help answer questions of the type
   'which proteins contain at least x occurrences of word X and y
   occurences of word Y in regions of n residues'. For example, one could
   search for serine rich or polyglutamine rich, collagen helix, or
   similar proteins using this program.

   oddcomp does not report the location of the word matches in the
   sequence, merely the sequence ID. To search for a specific set of words
   in a sequence, you should edit the input file of sequence word
   composition data.

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
   backtranambig    Back-translate a protein sequence to ambiguous nucleotide
                    sequence
   backtranseq      Back-translate a protein sequence to a nucleotide sequence
   compseq          Calculate the composition of unique words in sequences
   emowse           Search protein sequences by digest fragment molecular weight
   freak            Generate residue/base frequency table or plot
   mwcontam         Find weights common to multiple molecular weights files
   mwfilter         Filter noisy data from molecular weights file
   pepdigest        Report on protein proteolytic enzyme or reagent cleavage
                    sites
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   pepstats         Calculate statistics of protein properties
   wordcount        Count and extract unique words in molecular sequence(s)

Author(s)

   David Martin

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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
