Quicktandem

• QUICKTANDEM
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • ALGORITHM
  • INPUT FILE
  • COMMAND-LINE SUMMARY
  • OPTIONAL PARAMETERS
    • -ORIGinal

QUICKTANDEM

FUNCTION

QuickTandem scans for potential tandem repeats in a nucleotide sequence.

DESCRIPTION

QuickTandem scans a sequence for potential tandem repeats up to a specified size. The results can be used to run Tandem on the candidate repeat lengths to identify genuine tandem repeats.

To find repeated motifs with gaps between them, use the program ERepeat.

AUTHOR

This program was originally written by Richard Durbin and Jean Thierry-Mieg as part of the ACEDB genome database package.

This version was modified for inclusion in EGCG by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a sample session with QuickTandem

  
  
  % quicktandem
  
  
   QUICKTANDEM uses nucleotide sequence data
  
   QUICKTANDEM of what sequence ?  GenEMBL:hhtetra
  
                Start (* 1 *) ?
                End (* 1272 *) ?
  
   What maximum repeat size (* 600 *) ?
  
   What threshold score (* 20 *) ?
  
   What should I call the output file (* hhtetra.qtan *) ?
  %
  

OUTPUT

The output from QuickTandem is a simple report of hits in the sequence.

  
  
  QUICKTANDEM of em_vi:hhtetra check: 7108
  
   Score      Begin        End Length Ratio ..
  
339        191        935      6   124
  

ALGORITHM

INPUT FILE

The input file for QuickTandem is a GCG nucleotide sequence file.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum Syntax: % quicktandem [-INfile=]GenEmbl:hhtetra -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=100           Range of interest
  [-OUTfile=]hhtetra.qtan   Output file
  -MAXREPeat=600            Maximum repeat size
  -THRESHold=20             Minimum score
  
  Local Data Files: None
  
  Optional Parameters:
  
  
  -ORIGinal=stdout          Produce original mimimal output format
  

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-ORIGinal=stdout

requests the output format of the original quicktandem program, optionally with an output file name (the default is to write to the terminal).

Printed: April 22, 1996 15:55 (1162)