etandem

 

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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.

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 
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

Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
-minrepeat Minimum repeat size Integer, 2 or higher 10
-maxrepeat Maximum repeat size Integer, same as -minrepeat or higher Same as -minrepeat
[-outfile]
(Parameter 2)
Output report file name Report output file <*>.etandem
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-threshold Threshold score Any integer value 20
-mismatch Allow N as a mismatch Boolean value Yes/No No
-uniform Allow uniform consensus Boolean value Yes/No No
-origfile Sanger Centre program tandem output file (optional) Output file <*>.etandem

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; 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, 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)
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