| 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