Tandem
TANDEM
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)