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equicktandem |
equicktandem is a simple program that looks for segments in which each base tends to match the base 'repeatsize' back, i.e. with an autocorrelation peak at 'repeatsize'. This can allow drift in the repeating sequence, i.e. it does not look for a consensus sequence for the whole repeat block (that is what etandem does). But it is much quicker than etandem. It does not account for gaps.
The score is +1 for a match to the corresponding base 'repeatsize' back and -1 for a mismatch.
The input sequence is the human herpesvirus tandem repeat.
% equicktandem Finds tandem repeats Input sequence: tembl:hhtetra Maximum repeat size [600]: Threshold score [20]: Output report [hhtetra.qtan]: |
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Mandatory qualifiers: [-sequence] sequence Sequence USA -maxrepeat integer Maximum repeat size -threshold integer Threshold score [-outfile] report Output report file name Optional qualifiers: (none) Advanced qualifiers: -origfile outfile Output file name General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
-maxrepeat | Maximum repeat size | Any integer value | 600 |
-threshold | Threshold score | Any integer value | 20 |
[-outfile] (Parameter 2) |
Output report file name | Report output file | |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-origfile | Output file name | Output file | <sequence>.equicktandem |
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 // |
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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default equicktandem writes a 'table' report file.
######################################## # Program: equicktandem # Rundate: Thu Nov 07 14:23:56 2002 # Report_format: table # Report_file: hhtetra.qtan ######################################## #======================================= # # Sequence: HHTETRA from: 1 to: 1272 # HitCount: 1 # # Threshold: 20 # Maxrepeat: 600 # #======================================= Start End Score Size Count 191 935 339 6 124 #--------------------------------------- #--------------------------------------- |
Program name | Description |
---|---|
einverted | Finds DNA inverted repeats |
etandem | Looks for tandem repeats in a nucleotide sequence |
palindrome | Looks for inverted repeats in a nucleotide sequence |
equicktandem identifies regions wich are likely to contain tanden repeats. tandem should then be run on those regions to confirm them and to get an accurate specification of the repeats. tandem runs slowly.
This application was modified for inclusion in EMBOSS by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.