shuffleseq |
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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.
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
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 [ |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-sequence] (Parameter 1) |
seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-shuffle | integer | Number of shuffles | Any integer value | 1 |
Associated qualifiers | ||||
"-sequence" associated seqall qualifiers | ||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
-send1 -send_sequence |
integer | End of each 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 | |
"-outseq" associated seqoutall qualifiers | ||||
-osformat2 -osformat_outseq |
string | Output seq format | Any string | |
-osextension2 -osextension_outseq |
string | File name extension | Any string | |
-osname2 -osname_outseq |
string | Base file name | Any string | |
-osdirectory2 -osdirectory_outseq |
string | Output directory | Any string | |
-osdbname2 -osdbname_outseq |
string | Database name to add | Any string | |
-ossingle2 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
-oufo2 -oufo_outseq |
string | UFO features | Any string | |
-offormat2 -offormat_outseq |
string | Features format | Any string | |
-ofname2 -ofname_outseq |
string | Features file name | Any string | |
-ofdirectory2 -ofdirectory_outseq |
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 |
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.
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 // |
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.
>L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy chain mRNA. aggtttttatattacaagcatactaagagactcgcgatgatcgcacaattccaaatgtgc tcatgggtgtagcaagaacctcaaataaaagggcaaccatgagggtaaagtctccgcatg agcccctgggacgcgagagactttctcccgctagtgggtcgaacctgcagtgtcgataat tggagttaaaatcgcagcatttacggccatgaattgtgtcgatanacgattcacgcaatc gttaagatcaggttcattgggntcacaaaccgtaggccccccgttgcctgacgcgtaacg ttcggatttccgtgacttcatctgactactctgtcacattcttacacgacaagctcaaca agccgg >L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody 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.
shuffleseq is useful for producing sets of sequences with randomised order which can be used for checking the statistics of sequence similarity searches.
Program name | Description |
---|---|
msbar | Mutate a sequence |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.