
                            EMBOSS: equicktandem
     _________________________________________________________________
   
                             Program equicktandem
                                       
Function

   Finds tandem repeats
   
Description

   equicktandem scans a sequence for potential tandem repeats up to a
   specified size. The results can be used to run etandem on the
   candidate repeat lengths to identify genuine tandem repeats.
   
   equicktandem is a simple program that looks for segments in which each
   base tends to match the base 'repeatsize' back, i.e. with an
   autocorrelation peak at 'repeatsize'. This can allow drift in the
   repeating sequence, i.e. it does not look for a consensus sequence for
   the whole repeat block (that is what etandem does). But it is much
   quicker than etandem. It does not account for gaps.
   
   The score is +1 for a match to the corresponding base 'repeatsize'
   back and -1 for a mismatch.
   
Usage

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

% equicktandem
Input sequence: embl:hhtetra
Output file [hhtetra.qtan]:
Maximum repeat size [600]:
Threshold score [20]:

Command line arguments

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

   Optional qualifiers: (none)
   Advanced qualifiers:
   -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
   -maxrepeat Maximum repeat size Any integer value 600
   -threshold Threshold score Any integer value 20
   [-outfile]
   (Parameter 2) (no help text) report value Report file
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -origfile Output file name Output file <sequence>.equicktandem
   
Input file format

   The input for equicktandem 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 equicktandem writes a 'table' report file.
   
   The output from the above example is:
   
########################################
# Program: equicktandem
# Rundate: Thu Apr 11 13:28:55 2002
# Report_file: stdout
########################################

#=======================================
#
# Sequence: HHTETRA     from: 1   to: 1272
# HitCount: 1
#
# Threshold: 20
# Maxrepeat: 600
#
#=======================================

  Start     End   Score   Size  Count
    191     935     339      6    124

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

Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name                     Description
   einverted    Finds DNA inverted repeats
   etandem      Looks for tandem repeats in a nucleotide sequence
   palindrome   Looks for inverted repeats in a nucleotide sequence
   
   equicktandem identifies regions wich are likely to contain tanden
   repeats. tandem should then be run on those regions to confirm them
   and to get an accurate specification of the repeats. tandem runs
   slowly.
   
Author(s)

   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.
   
History

   Completed 25 May 1999
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
