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)

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:

  1. Score
  2. Start base position
  3. End base position
  4. Repeat size
  5. Repeat count
   339        191        935  6 124

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
chaosCreate a chaos game representation plot for a sequence
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
diffseqFind differences (SNPs) between nearly identical sequences
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
einvertedFinds DNA inverted repeats
etandemLooks for tandem repeats in a nucleotide sequence
isochorePlots isochores in large DNA sequences
newcpgreportReport CpG rich areas
newcpgseekReports CpG rich regions
palindromeLooks for inverted repeats in a nucleotide sequence
polydotDisplays all-against-all dotplots of a set of sequences
redataSearch REBASE for enzyme name, references, suppliers etc
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
silentSilent mutation restriction enzyme scan
tfscanScans 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.

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