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oddcomp
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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
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