etandem 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 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 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 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 // 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 #--------------------------------------- #--------------------------------------- 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 Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. Please report all bugs to the EMBOSS bug team (emboss-bug (c) 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 (c) emboss.open-bio.org) not to the original author. 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