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.

equicktandem is a simple program that looks for segments in which each base tends to match the base 'repeatsize' back, i.e. with an autocorrelation peak at 'repeatsize'. This can allow drift in the repeating sequence, i.e. it does not look for a consensus sequence for the whole repeat block (that is what etandem does). But it is much quicker than etandem. It does not account for gaps.

The score is +1 for a match to the corresponding base 'repeatsize' back and -1 for a mismatch.

Usage

Here is a sample session with equicktandem

The input sequence is the human herpesvirus tandem repeat.


% equicktandem 
Finds tandem repeats
Input sequence: tembl:hhtetra
Maximum repeat size [600]: 
Threshold score [20]: 
Output report [hhtetra.qtan]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
   -maxrepeat          integer    Maximum repeat size
   -threshold          integer    Threshold score
  [-outfile]           report     Output report file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -origfile           outfile    Output file name

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


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

Input file format

The input for equicktandem is a nucleotide sequence USA.

Input files for usage example

'tembl:hhtetra' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:hhtetra

ID   HHTETRA    standard; DNA; VRL; 1272 BP.
XX
AC   L46634; L46689;
XX
SV   L46634.1
XX
DT   06-NOV-1995 (Rel. 45, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 3)
XX
DE   Human herpesvirus 7 (clone ED132'1.2) telomeric repeat region.
XX
KW   telomeric repeat.
XX
OS   Human herpesvirus 7
OC   Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae.
XX
RN   [1]
RP   1-1272
RX   MEDLINE; 96079055.
RA   Secchiero P., Nicholas J., Deng H., Xiaopeng T., van Loon N., Ruvolo V.R.,
RA   Berneman Z.N., Reitz M.S. Jr., Dewhurst S.;
RT   "Identification of human telomeric repeat motifs at the genome termini of
RT   human herpesvirus 7: structural analysis and heterogeneity";
RL   J. Virol. 69(12):8041-8045(1995).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1272
FT                   /db_xref="taxon:10372"
FT                   /organism="Human herpesvirus 7"
FT                   /strain="JI"
FT                   /clone="ED132'1.2"
FT   repeat_region   207..928
FT                   /note="long and complex repeat region composed of various
FT                   direct repeats, including TAACCC (TRS), degenerate copies
FT                   of TRS motifs and a 14-bp repeat, TAGGGCTGCGGCCC"
FT   misc_signal     938..998
FT                   /note="pac2 motif"
FT   misc_feature    1009
FT                   /note="right genome terminus (...ACA)"
XX
SQ   Sequence 1272 BP; 346 A; 455 C; 222 G; 249 T; 0 other;
     aagcttaaac tgaggtcaca cacgacttta attacggcaa cgcaacagct gtaagctgca        60
     ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc       120
     tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa       180
     ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca       240
     actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc       300
     taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc       360
     taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc       420
     tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac       480
     cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc       540
     taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg       600
     gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc       660
     ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg       720
     cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac       780
     cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta       840
     accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta       900
     accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc       960
     cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac      1020
     gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt      1080
     agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga      1140
     aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca      1200
     agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa      1260
     gttttcaagc tt                                                          1272
//

Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default equicktandem writes a 'table' report file.

Output files for usage example

File: hhtetra.qtan

########################################
# Program: equicktandem
# Rundate: Thu Nov 07 14:23:56 2002
# Report_format: table
# Report_file: hhtetra.qtan
########################################

#=======================================
#
# Sequence: HHTETRA     from: 1   to: 1272
# HitCount: 1
#
# Threshold: 20
# Maxrepeat: 600
#
#=======================================

  Start     End   Score   Size  Count
    191     935     339      6    124

#---------------------------------------
#---------------------------------------

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program nameDescription
einvertedFinds DNA inverted repeats
etandemLooks for tandem repeats in a nucleotide sequence
palindromeLooks for inverted repeats in a nucleotide sequence

equicktandem identifies regions wich are likely to contain tanden repeats. tandem should then be run on those regions to confirm them and to get an accurate specification of the repeats. tandem runs slowly.

Author(s)

This program was originally written by Richard Durbin at the Sanger Centre.

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.

Comments