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EMBOSS: oddcomp |
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.
% oddcomp Finds protein sequence regions with a biased composition Input sequence(s): sw:* Output file [5h1d_fugru.oddcomp]: out.odd Input file: test.comp Window size to consider (e.g. 30 aa) [30]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-compdata] 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. Optional qualifiers: (none) Advanced qualifiers: -[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. 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 |
[-compdata] (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 |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced 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. | Yes/No | Yes |
# 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.
The output from the above example follows:
# # Output from 'oddcomp' # # The Expected frequencies are taken from the file: test.comp # # Word size: 2 CB1B_FUGRU CO9_FUGRU FOS_FUGRU RS7_FUGRU # END #
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
digest | Protein proteolytic enzyme or reagent cleavage digest |
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 |