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.

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
  [-outfile]           outfile    Output file name
   -maxrepeat          integer    Maximum repeat size
   -threshold          integer    Threshold score

   Optional qualifiers: (none)
   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

[-sequence]
(Parameter 1) Sequence USA Readable sequence Required

[-outfile]
(Parameter 2) Output file name Output file <sequence>.equicktandem

-maxrepeat Maximum repeat size Any integer value 600

-threshold Threshold score Any integer value 20

Optional qualifiers Allowed values Default

(none)

Advanced qualifiers Allowed values Default

(none)

Mandatory qualifiers	Allowed values	Default
[-sequence] (Parameter 1)	Sequence USA	Readable sequence	Required
[-outfile] (Parameter 2)	Output file name	Output file	<sequence>.equicktandem
-maxrepeat	Maximum repeat size	Any integer value	600
-threshold	Threshold score	Any integer value	20
Optional qualifiers	Allowed values	Default
(none)
Advanced qualifiers	Allowed values	Default
(none)

Input file format

The input for equicktandem is a nucleotide sequence

Output file format

The output from equicktandem is an uncommented list of identified repeats. In a future version this will change to be annotated sequence features.

The columns of the report show:

Score
Start base position
End base position
Repeat size
Repeat count

   339        191        935  6 124

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Program name	Description
chaos	Create a chaos game representation plot for a sequence
cpgplot	Plot CpG rich areas
cpgreport	Reports all CpG rich regions
diffseq	Find differences (SNPs) between nearly identical sequences
dotmatcher	Displays a thresholded dotplot of two sequences
dotpath	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	Displays a wordmatch dotplot of two sequences
einverted	Finds DNA inverted repeats
etandem	Looks for tandem repeats in a nucleotide sequence
isochore	Plots isochores in large DNA sequences
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
palindrome	Looks for inverted repeats in a nucleotide sequence
polydot	Displays all-against-all dotplots of a set of sequences
redata	Search REBASE for enzyme name, references, suppliers etc
restrict	Finds restriction enzyme cleavage sites
showseq	Display a sequence with features, translation etc
silent	Silent mutation RE scan
tfscan	Scans DNA sequences for transcription factors

Author(s)

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

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.