                                   etandem



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Find 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.

   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.

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
Find 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

Find tandem repeats in a nucleotide sequence
Version: EMBOSS:6.5.6.0

   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 (default
                                  -rformat table)

   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
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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


Input file format

   etandem reads a single nucleotide sequence.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

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

  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, dasgff, debug, listfile, dbmotif, diffseq,
   draw, restrict, excel, feattable, motif, nametable, 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: Sun 15 Jul 2012 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    Find inverted repeats in nucleotide sequences
   equicktandem     Find tandem repeats in nucleotide sequences
                    palindrome   Find 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
   Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
   CB10 1SA, UK.

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) 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 (c) 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
