
                                  etandem 



Function

   Finds tandem repeats in a nucleotide sequence

Description

   etandem identifies tandem repeats in a nucleotide sequence. It
   calculates a consensus sequence for a putative repeat region and
   scores potential repeats based on the number of matches and mismatches
   there are to the consensus. For a repeat to be identified, it must be
   within the specified minimum and maximum size and must score higher
   than the specified threshold score. The output is a standard EMBOSS
   report file with details of the location and score of any tandem
   repeats. Optionally, the output can be written in the format of the
   Sanger Centre quicktandem program.

Algorithm

   The input sequence is first converted so that it contains the
   characters ACGT or N only, i.e. any ambiguity codes are converted to
   N. etandem looks for sequence segments which match well to a consensus
   sequence calculated from non-overlapping windows over the sequence.
   For a given start point in the sequence and repeat size, a consensus
   sequence is built from contiguous sequence segments of that size.

   The score for a segment (except the first segment which is not scored)
   is based on the number of matches and mismatches there are to the
   consensus: the score is incremented (+1) for a match and decremented
   (-1) for a mismatch. By default, an "N" can never mismatch with a
   nucleotide but this behaviour can be changed with the -mismatch
   option. The highest scoring segment is kept for each start position
   and repeat size.

   Immediately adjacent segments that score higher than the specified
   threshold score are reported as a tandem repeat. The threshold score
   can be set on the command-line using the -threshold qualifier, the
   default is 20. For perfect repeats, the score is the equal to the
   length of the repeat. To allow for mismatches, the threshold score can
   be reduced. Each mismatch scores -1 instead of +1 so it scores 2 less
   than a perfect match of the same number of bases.

Usage

   Here is a sample session with etandem

   The input sequence is the human herpesvirus tandem repeat.


% etandem -noorigfile 
Finds tandem repeats in a nucleotide sequence
Input nucleotide sequence: tembl:L46634
Minimum repeat size [10]: 6
Maximum repeat size [6]: 
Output report [l46634.tan]: 

   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)
   -minrepeat          integer    [10] Minimum repeat size (Integer, 2 or
                                  higher)
   -maxrepeat          integer    [Same as -minrepeat] Maximum repeat size
                                  (Integer, same as -minrepeat or higher)
  [-outfile]           report     [*.etandem] Output report file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -threshold          integer    [20] Threshold score (Any integer value)
   -mismatch           boolean    Allow N as a mismatch
   -uniform            boolean    Allow uniform consensus
   -origfile           outfile    [*.etandem] Sanger Centre program tandem
                                  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 etandem 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 etandem writes a 'table' report file.

  Output files for usage example

  File: l46634.tan

########################################
# Program: etandem
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: etandem
#    -noorigfile
#    -sequence tembl:L46634
#    -minrepeat 6
# Report_format: table
# Report_file: l46634.tan
########################################

#=======================================
#
# Sequence: L46634     from: 1   to: 1272
# HitCount: 5
#
# Threshold: 20
# Minrepeat: 6
# Maxrepeat: 6
# Mismatch: No
# Uniform: No
#
#=======================================

  Start     End  Strand   Score   Size  Count Identity Consensus
    793     936       +     120      6     24     93.8 acccta
    283     420       +      90      6     23     84.8 taaccc
    432     485       +      38      6      9     90.7 ccctaa
    494     529       +      26      6      6     94.4 ccctaa
    568     597       +      24      6      5    100.0 aaccct

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

Data files

   None

Notes

   Running etandem with a wide range of repeat sizes is inefficient. It
   is normally used after equicktandem has been run to identify putative
   sizes and locations of repeats.

References

   None.

Warnings

   None.

Diagnostics

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

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

   Running with a wide range of repeat sizes is inefficient. That is why
   equicktandem was written - to give a rapid estimate of the major
   repeat sizes.

Authors

   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
