
                                seqmatchall 



Function

   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 
All-against-all comparison of a set of sequences
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 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 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: Sun 15 Jul 2007 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

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

   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 Match large sequences against one or more other sequences
   water        Smith-Waterman local alignment
   wordfinder   Match large sequences against one or more other sequences
   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
