|   | seqmatchall | 
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.
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
| 
   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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | 
| -wordsize | Word size | Integer 2 or more | 4 | 
| [-outfile] (Parameter 2) | Output alignment file name | Alignment output file | <*>.seqmatchall | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
The sequences must be either all protein or all nucleic acid.
| #Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ tembl:V00296 | 
| 
########################################
# 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 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.
| 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.