
                               equicktandem 



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

   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. 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

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; Herpesviridae; Betaherpesvirinae;
OC   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        6
0
     ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc       12
0
     tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa       18
0
     ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca       24
0
     actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc       30
0
     taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc       36
0
     taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc       42
0
     tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac       48
0
     cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc       54
0
     taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg       60
0
     gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc       66
0
     ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg       72
0
     cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac       78
0
     cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta       84
0
     accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta       90
0
     accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc       96
0
     cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac      102
0
     gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt      108
0
     agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga      114
0
     aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca      120
0
     agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa      126
0
     gttttcaagc tt                                                          127
2
//

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://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: Tue 15 Jul 2008 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)

   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
   (rd © sanger.ac.uk)
   Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
   CB10 1SA, UK.

   This application was modified for inclusion in EMBOSS by Peter Rice
   (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, 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

   None
