FUNCTION

Tandem looks for multiple tandem repeats of a given size in a nucleotide sequence.

DESCRIPTION

Tandem looks for tandem repeats in a sequence. For repeated motifs with a gap between, use 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 Tandem.

% tandem

 TANDEM uses nucleotide sequence data

 TANDEM of what sequence ?  GenEMBL:hhtetra

                   Start (* 1 *) ?
                   End (* 1272 *) ?

 Minimum repeat size (* 10 *) ?  6

 Maximum repeat size (* 6 *) ?

 What threshold score (* 20 *) ?

 Allow N as a mismatch (* No *) ?

 Allow uniform consensus (* No *) ?

 What should I call the output file (* hhtetra.tan *) ?

%

OUTPUT

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

TANDEM of em_vi:hhtetra check: 7108

 Score      Start        End Length Copies Percent ..

   120        793        936      6     24    93.8 ACCCTA
    90        283        420      6     23    84.8 TAACCC
    38        432        485      6      9    90.7 CCCTAA
    26        494        529      6      6    94.4 CCCTAA
    24        568        597      6      5   100.0 AACCCT

ALGORITHM

INPUT FILE

The input file for Tandem 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: % tandem [-INfile=]GenEmbl:hhtetra -Default

Prompted Parameters:

-BEGin=1 -END=100           Range of interest
[-OUTfile=]hhtetra.tan   Output file
-THRESHold=20            Score threshold
-MISmatch                Treat ambiguous positions as mismatches
-UNIform                 Allow a uniform consensus
-MINREPeat=10            Minimum repeat length
-MAXREPeat=10            Maximum repeat length

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 tandem program, optionally with an output file name (the default is to write to the terminal).

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