equicktandem

 

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Function

Finds tandem repeats in nucleotide sequences

Description

equicktandem identifies regions in a nucleotide sequence which are likely to contain tanden repeats. For a region to be reported, it must be no larger than a specified maximum repeat size and must score higher than a threshold score, which is also user-specified. The output is a standard EMBOSS report file with details of the location and score of any potential tandem repeats. Optionally, the output can be written in the format of the Sanger Centre quicktandem program.

Algorithm

equicktandem looks for sequence segments in which each base tends to match the base a fixed number ('repeatsize') of nucleotides back in the sequence, i.e. with an autocorrelation peak at 'repeatsize'. The score for a segment is the sum of the scores for each position in that segment: the score is incremented (+1) for a match to the corresponding base 'repeatsize' back and decremented (-1) for a mismatch. The algorithm allows for drift in the repeating sequence, i.e. exact matches are not required, nor is a consensus sequence for the whole repeat block used (that is what etandem does). The algorithm does not account for gaps but it is much quicker than etandem.

Usage

Here is a sample session with equicktandem

The input sequence is the human herpesvirus tandem repeat.


% equicktandem -noorigfile 
Finds tandem repeats in nucleotide sequences
Input nucleotide sequence: tembl:L46634
Maximum repeat size [600]: 
Threshold score [20]: 
Output report [l46634.qtan]: 

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

Command line arguments

Finds tandem repeats in nucleotide sequences
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
   -maxrepeat          integer    [600] Maximum repeat size (Any integer
                                  value)
   -threshold          integer    [20] Threshold score (Any integer value)
  [-outfile]           report     [*.equicktandem] Output report file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -origfile           outfile    [*.equicktandem] Sanger Centre program
                                  quicktandem output file (optional)

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   "-origfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)
sequence Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
-maxrepeat integer Maximum repeat size Any integer value 600
-threshold integer Threshold score Any integer value 20
[-outfile]
(Parameter 2)
report Output report file name Report output file <*>.equicktandem
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-origfile outfile Sanger Centre program quicktandem output file (optional) Output file <*>.equicktandem
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1
-sbegin_sequence
integer Start of the sequence to be used Any integer value 0
-send1
-send_sequence
integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-sdbname1
-sdbname_sequence
string Database name Any string  
-sid1
-sid_sequence
string Entryname Any string  
-ufo1
-ufo_sequence
string UFO features Any string  
-fformat1
-fformat_sequence
string Features format Any string  
-fopenfile1
-fopenfile_sequence
string Features file name Any string  
"-outfile" associated report qualifiers
-rformat2
-rformat_outfile
string Report format Any string table
-rname2
-rname_outfile
string Base file name Any string  
-rextension2
-rextension_outfile
string File name extension Any string qtan
-rdirectory2
-rdirectory_outfile
string Output directory Any string  
-raccshow2
-raccshow_outfile
boolean Show accession number in the report Boolean value Yes/No N
-rdesshow2
-rdesshow_outfile
boolean Show description in the report Boolean value Yes/No N
-rscoreshow2
-rscoreshow_outfile
boolean Show the score in the report Boolean value Yes/No Y
-rstrandshow2
-rstrandshow_outfile
boolean Show the nucleotide strand in the report Boolean value Yes/No Y
-rusashow2
-rusashow_outfile
boolean Show the full USA in the report Boolean value Yes/No N
-rmaxall2
-rmaxall_outfile
integer Maximum total hits to report Any integer value 0
-rmaxseq2
-rmaxseq_outfile
integer Maximum hits to report for one sequence Any integer value 0
"-origfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

The input for equicktandem is a nucleotide sequence USA.

Input files for usage example

'tembl:L46634' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:L46634

ID   L46634; SV 1; linear; genomic DNA; STD; VRL; 1272 BP.
XX
AC   L46634; L46689;
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; Herpesvirales; Herpesviridae;
OC   Betaherpesvirinae; Roseolovirus.
XX
RN   [1]
RP   1-1272
RX   PUBMED; 7494318.
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                   /organism="Human herpesvirus 7"
FT                   /strain="JI"
FT                   /mol_type="genomic DNA"
FT                   /clone="ED132'1.2"
FT                   /db_xref="taxon:10372"
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, debug, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.

By default equicktandem writes a 'table' report file.

Output files for usage example

File: l46634.qtan

########################################
# Program: equicktandem
# Rundate: Fri 15 Jan 2010 12:00:00
# Commandline: equicktandem
#    -noorigfile
#    -sequence tembl:L46634
# Report_format: table
# Report_file: l46634.qtan
########################################

#=======================================
#
# Sequence: L46634     from: 1   to: 1272
# HitCount: 1
#
# Threshold: 20
# Maxrepeat: 600
#
#=======================================

  Start     End  Strand   Score   Size  Count
    191     935       +     339      6    124

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

Data files

None.

Notes

A tandem repeat in a DNA sequence is where a sequence of two or more nucleotides is repeated without any intervening nucleotides. For example "GATACAGATACAGATACA" is a tandem repeat of "GATACA". A short tandem repeat is typically 2 to 10 base pairs and occur in introns. The sequence and number of repeats at a given locus tend to be characteristic of an individual. Where enough STR loci are examined, a unique genetic profile of an individual can be built. Thus, tandem repeats are useful for genotyping, for example, in determining parentage and in forensic cases.

To identify genuine tandem repeats, the repeat sizes and / or sequence regions identified by equicktandem can be used as input to etandem. etandem will confirm which regions are true tandem repeats and give an accurate specification of the repeats.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
einverted Finds inverted repeats in nucleotide sequences
etandem Finds tandem repeats in a nucleotide sequence
palindrome Finds inverted repeats in nucleotide sequence(s)

Author(s)

This program was originally written by Richard Durbin
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

This application was modified for inclusion in EMBOSS by Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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

None