Tehdyt toimenpiteet
|
equicktandem |
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
Finds tandem repeats in nucleotide sequencesDescription
equicktandem identifies regions in a nucleotide sequence which are likely to contain tanden repeats. For a region to be reported, it must be no larger than a specified maximum repeat size and must score higher than a threshold score, which is also user-specified. The output is a standard EMBOSS report file with details of the location and score of any potential tandem repeats. Optionally, the output can be written in the format of the Sanger Centre quicktandem program.
Algorithm
equicktandem looks for sequence segments in which each base tends to match the base a fixed number ('repeatsize') of nucleotides back in the sequence, i.e. with an autocorrelation peak at 'repeatsize'. The score for a segment is the sum of the scores for each position in that segment: the score is incremented (+1) for a match to the corresponding base 'repeatsize' back and decremented (-1) for a mismatch. The algorithm allows for drift in the repeating sequence, i.e. exact matches are not required, nor is a consensus sequence for the whole repeat block used (that is what etandem does). The algorithm does not account for gaps but it is much quicker than etandem.
Usage
Here is a sample session with equicktandemThe input sequence is the human herpesvirus tandem repeat.
% equicktandem -noorigfile Finds tandem repeats in nucleotide sequences Input nucleotide sequence: tembl:L46634 Maximum repeat size [600]: Threshold score [20]: Output report [l46634.qtan]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Finds tandem repeats in nucleotide sequences
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
-maxrepeat integer [600] Maximum repeat size (Any integer
value)
-threshold integer [20] Threshold score (Any integer value)
[-outfile] report [*.equicktandem] Output report file name
(default -rformat table)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-origfile outfile [*.equicktandem] Sanger Centre program
quicktandem 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 |
| -maxrepeat | integer | Maximum repeat size | Any integer value | 600 |
| -threshold | integer | Threshold score | Any integer value | 20 |
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat table) | <*>.equicktandem |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -origfile | outfile | Sanger Centre program quicktandem output file (optional) | Output file | <*>.equicktandem |
| 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 | qtan |
| -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
equicktandem 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 equicktandem writes a 'table' report file.
Output files for usage example
File: l46634.qtan
########################################
# Program: equicktandem
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: equicktandem
# -noorigfile
# -sequence tembl:L46634
# Report_format: table
# Report_file: l46634.qtan
########################################
#=======================================
#
# Sequence: L46634 from: 1 to: 1272
# HitCount: 1
#
# Threshold: 20
# Maxrepeat: 600
#
#=======================================
Start End Strand Score Size Count
191 935 + 339 6 124
#---------------------------------------
#---------------------------------------
|
Data files
None.Notes
A tandem repeat in a DNA sequence is where a sequence of two or more nucleotides is repeated without any intervening nucleotides. For example "GATACAGATACAGATACA" is a tandem repeat of "GATACA". A short tandem repeat is typically 2 to 10 base pairs and occur in introns. The sequence and number of repeats at a given locus tend to be characteristic of an individual. Where enough STR loci are examined, a unique genetic profile of an individual can be built. Thus, tandem repeats are useful for genotyping, for example, in determining parentage and in forensic cases.
To identify genuine tandem repeats, the repeat sizes and / or sequence regions identified by equicktandem can be used as input to etandem. etandem will confirm which regions are true tandem repeats and give an accurate specification of the repeats.
References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with a status of 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| einverted | Finds inverted repeats in nucleotide sequences |
| etandem | Finds tandem repeats in a nucleotide sequence |
| palindrome | Finds inverted repeats in nucleotide sequence(s) |
Author(s)
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.