
                                seqmatchall 



Function

   All-against-all word comparison of a sequence set

Description

   seqmatchall takes a set of sequences and does an all-against-all
   pairwise comparison of words of a specified size in the sequences,
   finding regions of identity between any two sequences. It writes an
   output file with a list of regions of identity in pairs of sequences,
   the start and end positions and length of the matching regions and the
   name of the sequences.

Usage

   Here is a sample session with seqmatchall

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


% seqmatchall 
All-against-all word comparison of a sequence set
Input sequence set: @eclac.list
Word size [4]: 15
Output alignment [j01636.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 filename and optional format,
                                  or reference (input USA)
   -wordsize           integer    [4] Word size (Integer 2 or more)
  [-outfile]           align      [*.seqmatchall] 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 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. 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

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

  File: eclac.list

#Formerly ECLAC
tembl:J01636

#Formerly ECLACA
tembl:X51872

#Formerly ECLACI
tembl:V00294

#Formerly ECLACY
tembl:V00295

#Formerly ECLACZ
tembl:V00296

Output file format

  Output files for usage example

  File: j01636.seqmatchall

########################################
# Program: seqmatchall
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: seqmatchall
#    -sequence @../../data/eclac.list
#    -wordsize 15
# Align_format: match
# Report_file: j01636.seqmatchall
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: X51872
#=======================================

  1832 J01636          +     5646..7477     X51872          +        1..1832

#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: V00294
#=======================================

  1113 J01636          +       49..1161     V00294          +        1..1113

#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: V00295
#=======================================

  1500 J01636          +     4305..5804     V00295          +        1..1500

#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: V00296
#=======================================

  3078 J01636          +     1287..4364     V00296          +        1..3078

#=======================================
#
# Aligned_sequences: 2
# 1: X51872
# 2: V00295
#=======================================

   159 X51872          +        1..159      V00295          +     1342..1500

#=======================================
#
# Aligned_sequences: 2
# 1: V00295
# 2: V00296
#=======================================

    60 V00295          +        1..60       V00296          +     3019..3078

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

   J01636 (the complete E.coli lac operon) matches V00294 V00295 V00296
   and X51872 (the individual genes), and there is a short overlap
   between V00295 (lacY) and the flanking genes V00296 (lacZ) and X51872
   (lacA)

   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 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.

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 Waterman-Eggert local alignment of two sequences
   supermatcher Calculate approximate local pair-wise alignments of
   larger sequences
   water Smith-Waterman local alignment of sequences
   wordfinder Match large sequences against one or more other sequences
   wordmatch Finds regions of identity (exact matches) of two 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
