| ## EMBOSS: etandem

# Program etandem

## Function

Looks for tandem repeats in a nucleotide sequence

## Description

etandem looks for tandem repeats in a sequence. It is normally used after equicktandem has been run to identify potential repeat sizes. It calculates a consensus for the repeat region and gives a score for how many matches there are to the consensus - the number of mismatches.

Input sequences are converted into ACGT or N (so ambiguity codes are ignored).
The score is +1 for a match, -1 for a mismatch.
The first copy of a repeat is ignored.
The highest score is kept for each start position and repeat size.

The lowest score to be reported is set by the threshold score. The threshold score can be set on the command-line using the -threshold qualifier, the default is 20. For perfect repeats, the score is the length of the repeat (except for the first copy). Reduce the threshold score a little if you wish to to allow mismatches. Each mismatch scores -1 instead of +1 so it scores 2 less than a perfect match of the same number of bases.

Running with a wide range of repeat sizes is inefficient. That is why equicktandem was written - to give a rapid estimate of the major repeat sizes.

## Usage

Here is a sample session with etandem. The input sequence is the human herpesvirus tandem repeat.

    % etandem
    Input sequence: embl:hhtetra
    Output file [hhtetra.tan]:
    Minimum repeat size [10]: 6
    Maximum repeat size [6]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          sequence   Sequence USA
       -minrepeat          integer    Minimum repeat size
       -maxrepeat          integer    Maximum repeat size
      [-outfile]           report     (no help text) report value

       Optional qualifiers: (none)
       Advanced qualifiers:
       -threshold          integer    Threshold score
       -mismatch           bool       Allow N as a mismatch
       -uniform            bool       Allow uniform consensus
       -origfile           outfile    Output file name

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence USA | Readable sequence | Required
-minrepeat | Minimum repeat size | Integer, 2 or higher | 10
-maxrepeat | Maximum repeat size | Integer, same as -minrepeat or higher | Same as -minrepeat
[-outfile] (Parameter 2) | (no help text) report value | Report file |
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-threshold | Threshold score | Any integer value | 20
-mismatch | Allow N as a mismatch | Yes/No | No
-uniform | Allow uniform consensus | Yes/No | No
-origfile | Output file name | Output file | <sequence>.etandem

## Input file format

The input for etandem is a nucleotide sequence.

## Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default etandem writes a 'table' report file.

The output from the above example is:

    ########################################
    # Program: etandem
    # Rundate: Thu Apr 11 13:31:10 2002
    # Report_file: stdout
    ########################################

    #=======================================
    #
    # Sequence: HHTETRA     from: 1   to: 1272
    # HitCount: 5
    #
    # Threshold: 20
    # Minrepeat: 6
    # Maxrepeat: 6
    # Mismatch: No
    # Uniform: No
    #
    #=======================================

      Start     End   Score   Size  Count Identity Consensus
        793     936     120      6     24     93.8 acccta
        283     420      90      6     23     84.8 taaccc
        432     485      38      6      9     90.7 ccctaa
        494     529      26      6      6     94.4 ccctaa
        568     597      24      6      5    100.0 aaccct

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

## Data files

## Notes

Running with a wide range of repeat sizes is inefficient. That is why equicktandem was written - to give a rapid estimate of the major repeat sizes.

## References

None.

## Warnings

None.

## Diagnostics

None.

## Exit status

None.

## Known bugs

None.

## See also

Program name | Description
--- | ---
einverted | Finds DNA inverted repeats
equicktandem | Finds tandem repeats
palindrome | Looks for inverted repeats in a nucleotide sequence

Running with a wide range of repeat sizes is inefficient. That is why equicktandem was written - to give a rapid estimate of the major repeat sizes.

## Authors

This program was originally written by Richard Durbin at the Sanger Centre.

This application was modified for inclusion in EMBOSS by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## Priority

Completed 25 May 1999

## Target

etandem is aimed at automated repeat identification in genomic sequnece but can also be used by general users.

## Comments