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etandem |
Function
Looks for tandem repeats in a nucleotide sequenceDescription
etandem looks for tandem repeats in a sequence. It is normally used after equicktandem has been run to identify potential repeat sizes. It calculates a consensus for the repeat region and gives a score for how many matches there are to the consensus - the number of mismatches.
Input sequences are converted into ACGT or N (so ambiguity codes are ignored).
The score is +1 for a match, -1 for a mismatch.
The first copy of a repeat is ignored.
The highest score is kept for each start position and repeat size.
The lowest score to be reported is set by the threshold score. 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 length of the repeat (except for the first copy). Reduce the threshold score a little if you wish to to allow mismatches. Each mismatch scores -1 instead of +1 so it scores 2 less than a perfect match of the same number of bases.
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.
Usage
Here is a sample session with etandemThe input sequence is the human herpesvirus tandem repeat.
% etandem -noorigfile Looks for tandem repeats in a nucleotide sequence Input sequence: tembl:hhtetra Minimum repeat size [10]: 6 Maximum repeat size [6]: Output report [hhtetra.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 Sequence USA
-minrepeat integer Minimum repeat size
-maxrepeat integer Maximum repeat size
[-outfile] report Output report file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-threshold integer Threshold score
-mismatch boolean Allow N as a mismatch
-uniform boolean Allow uniform consensus
-origfile outfile Output file name
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
-rusashow2 boolean Show the full USA in the report
"-origfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence 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 | |
| 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 | Output file name | Output file | <sequence>.etandem |
Input file format
The input for etandem is a nucleotide sequence USA.Input files for usage example
'tembl:hhtetra' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:hhtetra
ID HHTETRA standard; DNA; VRL; 1272 BP.
XX
AC L46634; L46689;
XX
SV L46634.1
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.
XX
RN [1]
RP 1-1272
RX MEDLINE; 96079055.
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 /db_xref="taxon:10372"
FT /organism="Human herpesvirus 7"
FT /strain="JI"
FT /clone="ED132'1.2"
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
//
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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: hhtetra.tan
########################################
# Program: etandem
# Rundate: Fri Jul 15 2005 12:00:00
# Report_format: table
# Report_file: hhtetra.tan
########################################
#=======================================
#
# Sequence: HHTETRA from: 1 to: 1272
# HitCount: 5
#
# Threshold: 20
# Minrepeat: 6
# Maxrepeat: 6
# Mismatch: No
# Uniform: No
#
#=======================================
Start End 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
#---------------------------------------
#---------------------------------------
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Data files
NoneNotes
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.References
None.Warnings
None.Diagnostics
None.Exit status
It always exits with status 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| einverted | Finds DNA inverted repeats |
| equicktandem | Finds tandem repeats |
| palindrome | Looks for inverted repeats in a nucleotide sequence |
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