
                                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

   Here is an example using an increased word size to avoid accidental
   matches:


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

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     Sequence set USA
   -wordsize           integer    Word size
  [-outfile]           align      Output alignment file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   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
   -aformat2            string     Alignment format
   -aextension2         string     File name extension
   -adirectory2         string     Output directory
   -aname2              string     Base file name
   -awidth2             integer    Alignment width
   -aaccshow2           boolean    Show accession number in the header
   -adesshow2           boolean    Show description in the header
   -ausashow2           boolean    Show the full USA in the alignment
   -aglobal2            boolean    Show the full sequence in alignment

   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 set USA Readable set of sequences Required
   -wordsize Word size Integer 2 or more 4
   [-outfile]
   (Parameter 2) Output alignment file name Alignment output file
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   seqmatchall reads a set of sequence USAs.

   The sequences must be either all protein or all nucleic acid.

  Input files for usage example

   'tembl:eclac*' is a sequence entry in the example nucleic acid
   database 'tembl'

Output file format

  Output files for usage example

  File: eclac.seqmatchall

########################################
# Program: seqmatchall
# Rundate: Thu Jul 15 2004 12:00:00
# Align_format: match
# Report_file: eclac.seqmatchall
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: ECLAC
# 2: ECLACA
#=======================================

  1832 ECLAC           +     5646..7477     ECLACA          +        1..1832

#=======================================
#
# Aligned_sequences: 2
# 1: ECLAC
# 2: ECLACI
#=======================================

  1113 ECLAC           +       49..1161     ECLACI          +        1..1113

#=======================================
#
# Aligned_sequences: 2
# 1: ECLAC
# 2: ECLACY
#=======================================

  1500 ECLAC           +     4305..5804     ECLACY          +        1..1500

#=======================================
#
# Aligned_sequences: 2
# 1: ECLAC
# 2: ECLACZ
#=======================================

  3078 ECLAC           +     1287..4364     ECLACZ          +        1..3078

#=======================================
#
# Aligned_sequences: 2
# 1: ECLACA
# 2: ECLACY
#=======================================

   159 ECLACA          +        1..159      ECLACY          +     1342..1500

#=======================================
#
# Aligned_sequences: 2
# 1: ECLACY
# 2: ECLACZ
#=======================================

    60 ECLACY          +        1..60       ECLACZ          +     3019..3078

#---------------------------------------
#---------------------------------------

   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

   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

   None.

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

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It exits with a status of 0.

Known bugs

   None.

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)

   Ian Longden (il © sanger.ac.uk)
   Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
   CB10 1SA, UK.

History

   1999 - written - Ian Longden

Target users

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

Comments

   None
