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etandem |
Wiki
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Function
Finds tandem repeats in a nucleotide sequenceDescription
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 etandemThe 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
Finds tandem repeats in a nucleotide sequence
Version: EMBOSS:6.4.0.0
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
-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 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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| -minrepeat | integer | Minimum repeat size | Integer, 2 or higher | 10 |
| -maxrepeat | integer | Maximum repeat size | Integer, same as -minrepeat or higher | Same as -minrepeat |
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat table) | <*>.etandem |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -threshold | integer | Threshold score | Any integer value | 20 |
| -mismatch | boolean | Allow N as a mismatch | Boolean value Yes/No | No |
| -uniform | boolean | Allow uniform consensus | Boolean value Yes/No | No |
| -origfile | outfile | Sanger Centre program tandem output file (optional) | Output file | <*>.etandem |
| Associated qualifiers | ||||
| "-sequence" associated sequence qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of the sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated report qualifiers | ||||
| -rformat2 -rformat_outfile |
string | Report format | Any string | table |
| -rname2 -rname_outfile |
string | Base file name | Any string | |
| -rextension2 -rextension_outfile |
string | File name extension | Any string | tan |
| -rdirectory2 -rdirectory_outfile |
string | Output directory | Any string | |
| -raccshow2 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N |
| -rdesshow2 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N |
| -rscoreshow2 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | Y |
| -rstrandshow2 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y |
| -rusashow2 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N |
| -rmaxall2 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 |
| -rmaxseq2 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 |
| "-origfile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
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
//
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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, 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: Fri 15 Jul 2011 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
#---------------------------------------
#---------------------------------------
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Data files
NoneNotes
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 DurbinSanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Please report all bugs to the EMBOSS bug team (emboss-bug © 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 © emboss.open-bio.org) not to the original author.