
                            EMBOSS: seqmatchall
     _________________________________________________________________
   
                              Program seqmatchall
                                       
Function

   Does an all-against-all comparison of a set of sequences
   
Description

   This takes a set of sequences and does an all-against-all pairwise
   comparison of words (fragments of the sequences of a specified fixed
   size) in the sequences, finding regions of identity between any two
   sequences.
   
   The larger the specified word size, the faster the comparison will
   proceed. Regions whose stretches of identity are shorter than the word
   size will be missed. You should therefore choose a word size that is
   small enough to find those regions of similarity you are interested in
   within a reasonable time-frame.
   
Usage

   Here is a sample session with seqmatchall. We use an increased word
   size to avoid accidental matches.

% seqmatchall
Does an all-against-all comparison of a set of sequences
Input sequence set: embl:eclac*
Word size [4]: 15
Output file [outfile.seqmatchall]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqset     Sequence set USA
   -wordsize           integer    Word size
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   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 set USA Readable sequences Required
   -wordsize Word size Integer 2 or more 4
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.seqmatchall
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   A set of sequences. This can be a list file of sequence or a
   wildcarded set of sequences from a database or all sequences from a
   database, or a wildcarded set of sequence files.
   
   The sequences must be all either protein or nucleic.
   
Output file format

   Here is the output from the example run.
   
   ECLAC (the complete E.coli lac operon) matches ECLACI ECLACZ ECLACY
   and ECLACA (the individual genes), and there is a short overlap
   between ECLACY and the flanking genes ECLACZ and ECLACA

1832  5645 7477 ECLAC 0 1832 ECLACA
1113  48 1161 ECLAC 0 1113 ECLACI
1500  4304 5804 ECLAC 0 1500 ECLACY
3078  1286 4364 ECLAC 0 3078 ECLACZ
158  1 159 ECLACA 1342 1500 ECLACY
59  1 60 ECLACY 3019 3078 ECLACZ

   The output is a list of regions of identity in pairs of sequences,
   each consisting of one line with 7 columns of data separated by TABs
   or space characters. The columns of data consist of:
     * The length of the region of identity.
     * The start position in sequence 1.
     * The end position in sequence 1.
     * The name of sequence 1.
     * The start position in sequence 2.
     * The end position in sequence 2.
     * The name of sequence 2.
       
Data files

Notes

   The larger the word size, the faster the comparisons will proceed, but
   regions of identitly smaller than the word size will not be reported.
   
References

Warnings

Diagnostic Error Messages

Exit status

   It exits with a status of 0.
   
Known bugs

See also

   Program name Description
   matcher Finds the best local alignments between two sequences
   supermatcher Finds a match of a large sequence against one or more
   sequences
   water Smith-Waterman local alignment
   wordmatch Finds all exact matches of a given size between 2 sequences
   
   polydot will give a graphical view of the same matches.
   
Author(s)

   This application was written by Ian Longden (il@sanger.ac.uk)
   Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus,
   Hinxton, Cambridge, CB10 1SA, UK.
   
History

Target users

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