| seqmatchall

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## 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

    All-against-all word comparison of a sequence set
    Version: EMBOSS:6.6.0.0

       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
                                      (default -aformat match)

       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
       -scircular1         boolean    Sequence is circular
       -squick1            boolean    Read id and sequence only
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -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 and exit. 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
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqset | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
-wordsize | integer | Word size | Integer 2 or more | 4
[-outfile] (Parameter 2) | align | Output alignment file name | (default -aformat match) | <*>.seqmatchall
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated align qualifiers
-aformat2 -aformat_outfile | string | Alignment format | Any string | match
-aextension2 -aextension_outfile | string | File name extension | Any string |
-adirectory2 -adirectory_outfile | string | Output directory | Any string |
-aname2 -aname_outfile | string | Base file name | Any string |
-awidth2 -awidth_outfile | integer | Alignment width | Any integer value | 0
-aaccshow2 -aaccshow_outfile | boolean | Show accession number in the header | Boolean value Yes/No | N
-adesshow2 -adesshow_outfile | boolean | Show description in the header | Boolean value Yes/No | N
-ausashow2 -ausashow_outfile | boolean | Show the full USA in the alignment | Boolean value Yes/No | N
-aglobal2 -aglobal_outfile | boolean | Show the full sequence in alignment | Boolean value Yes/No | N
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

seqmatchall reads a set of nucleotide or protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### 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

The output is a standard EMBOSS alignment file.

The results can be output in one of several styles by using the command-line qualifier `-aformat xxx`, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences.

The available multiple alignment format names are: multiple, simple, fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip, phylipnon, selex, treecon, tcoffee, debug, srs.

The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, match, sam, bam, score, srspair

See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats.

By default the output is in 'match' format.

### Output files for usage example

### File: j01636.seqmatchall

    ########################################
    # Program: seqmatchall
    # Rundate: Mon 15 Jul 2013 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 | Find regions of identity (exact matches) of two sequences

polydot will give a graphical view of the same matches.

## Author(s)

Ian Longden formerly at:
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## 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