shuffleseq 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 Shuffles a set of sequences maintaining composition Description shuffleseq reads one or more sequences and writes them out again in a random (shuffled) order. The number of shuffles may be specified. Only the order of sequences is changed, no bases or residues are changed. Usage Here is a sample session with shuffleseq This makes two randomised copies of the input sequence: % shuffleseq -shuffle 2 Shuffles a set of sequences maintaining composition Input sequence(s): tembl:L48662 output sequence(s) [l48662.fasta]: Go to the input files for this example Go to the output files for this example Command line arguments Shuffles a set of sequences maintaining composition Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Sequence(s) filename and optional format, or reference (input USA) [-outseq] seqoutall [.] Sequence set(s) filename and optional format (output USA) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -shuffle integer [1] Number of shuffles (Any integer value) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each 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 "-outseq" associated qualifiers -osformat2 string Output seq format -osextension2 string File name extension -osname2 string Base file name -osdirectory2 string Output directory -osdbname2 string Database name to add -ossingle2 boolean Separate file for each entry -oufo2 string UFO features -offormat2 string Features format -ofname2 string Features file name -ofdirectory2 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 shuffleseq reads one or more nucleotide or protein sequences. 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:L48662' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:L48662 ID L48662; SV 1; linear; mRNA; STD; MUS; 366 BP. XX AC L48662; XX DT 04-NOV-1995 (Rel. 45, Created) DT 04-MAR-2000 (Rel. 63, Last updated, Version 4) XX DE Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy DE chain mRNA. XX KW . XX OS Mus musculus (house mouse) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; OC Muridae; Murinae; Mus. XX RN [1] RP 1-366 RX DOI; 10.1002/eji.1830260939. RX PUBMED; 8814271. RA Wloch M.K., Alexander A.L., Pippen A.M., Pisetsky D.S., Gilkeson G.S.; RT "Differences in V kappa gene utilization and VH CDR3 sequence among RT anti-DNA from C3H-lpr mice and lupus mice with nephritis"; RL Eur. J. Immunol. 26(9):2225-2233(1996). XX DR IMGT/LIGM; L48662. XX FH Key Location/Qualifiers FH FT source 1..366 FT /organism="Mus musculus" FT /strain="C3H/HeJ-lpr/lpr" FT /mol_type="mRNA" FT /cell_line="C3H/F2-11" FT /cell_type="hybridoma" FT /tissue_type="spleen" FT /db_xref="taxon:10090" XX SQ Sequence 366 BP; 100 A; 90 C; 85 G; 89 T; 2 other; gagnnccagc tgcagcagtc tggacctgag ctggtaaagc ctggggcttc agtgaagatg 60 tcctgcaagg cttctggata cacattcact agctatgtta tgcactgggt gaatcagaag 120 cctgggcagg gccttgagtg gattggatat attaatcctt acaatgatgg tactaactac 180 aatgagaagt tcaaaggcaa ggccacactg acttcagaca aatcctccag cacagcctac 240 atggagttca gcagcctgac ctctgaggac tctgcggtct attactgtgc aagaaaaact 300 tcctactata gtaacctata ttactttgac tactggggcc aaggcaccac tctcacagtc 360 tcctca 366 // Output file format The output is a standard EMBOSS sequence file. The results can be output in one of several styles by using the command-line qualifier -osformat 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, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Output files for usage example File: l48662.fasta >L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antib ody heavy chain mRNA. aggtttttatattacaagcatactaagagactcgcgatgatcgcacaattccaaatgtgc tcatgggtgtagcaagaacctcaaataaaagggcaaccatgagggtaaagtctccgcatg agcccctgggacgcgagagactttctcccgctagtgggtcgaacctgcagtgtcgataat tggagttaaaatcgcagcatttacggccatgaattgtgtcgatanacgattcacgcaatc gttaagatcaggttcattgggntcacaaaccgtaggccccccgttgcctgacgcgtaacg ttcggatttccgtgacttcatctgactactctgtcacattcttacacgacaagctcaaca agccgg >L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antib ody heavy chain mRNA. gtggatggtatccctaacccatgacttgcgattccattgactaataccgatttcgctatg cgaataatactgcacaataagcgctgggggttggtttaaanttgcgatgtattatcaggt gcatcatacgcgtgtcttcaatcgcaggagaatacaaactcagtcccaagcctaaggcgc gtgagacttcattagggcaacggatactgctaactagttaaactcgcatgtaacaactca cctgagcggtcgtacatgggcctctcttcccgaagggttgttcgaaaaaagcattgatac aggccaggcaagcaccacgtgtcagcactacgatggccgttntcaaagtagctcatacag cctcgc Each run will produce a different sequence. Note that these two sequences have the same name. Data files None. Notes shuffleseq is useful for producing sets of sequences with randomised order which can be used for checking the statistics of sequence similarity searches. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description msbar Mutate a sequence Author(s) Michael Schmitz formerly at: Lawrence Berkeley Labs, USA Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None