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shuffleseq |
The number of shuffled sequences output can be set by the '-shuffle' qualifier.
This makes two randomised copies of the input sequence:
% shuffleseq -shuffle 2 Shuffles a set of sequences maintaining composition Input sequence(s): tembl:mmam Output sequence [mmam.fasta]: |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outseq] seqoutall Output sequence(s) USA Optional qualifiers: (none) Advanced qualifiers: -shuffle integer Number of shuffles 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 database USA | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
Output sequence(s) USA | Writeable sequence(s) | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-shuffle | Number of shuffles | Any integer value | 1 |
ID MMAM standard; RNA; MUS; 366 BP. XX AC L48662; XX SV L48662.1 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; Rodentia; Sciurognathi; Muridae; Murinae; Mus. XX RN [1] RP 1-366 RX MEDLINE; 96409289. 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 FH Key Location/Qualifiers FH FT source 1..366 FT /db_xref="taxon:10090" FT /organism="Mus musculus" FT /strain="C3H/HeJ-lpr/lpr" FT /cell_line="C3H/F2-11" FT /cell_type="hybridoma" FT /tissue_type="spleen" 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 // |
>MMAM L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy chain mRNA. caatccaaacgcagtggttgccgagcccggaagaaccctctagggttattacttacagct gacactggggtagagcggtccagcagtgttagtcttgcagtgtctgtctatcggacaagc ggtcataggaactcagcagatccctcctggatcgacacaccaacgagtagattcgatcta gctgttagcgacctaatatcaacttcactaccgccgaaccaataagctaccggctttaac acgcgatatttcccatagatccaataaacaatttcatgtggtttggggaaaaaaactttg ccagtaatttggcngtgacgccatcccaatggngagtgcataaaatgtggtggcgcgcat tatttc >MMAM L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy chain mRNA. tgttctctagaaaatcacgacatttgtggtgtaccaggccctcgcggaaacgcggtaaaa aaacgataactggccaggcgagaacataaggcaatctagagagcgacaganggggaaccg agttgtgcgccagtttatctatcgggcggtcgcgcccgcttcctccccaaaacttaacgg agctgcacattaacgtggctgacgatactatttacccagatagccttggttccttagatt cgaagttgcactgttgtagacgagtggaaataaagtccgcatattacttaaatccgngtc actggatgctatctatgtattctactacactagctggctcacacatagataactccctta ccggct |
Each run will produce a different sequence.
Note that these two sequences have the same name.
Program name | Description |
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msbar | Mutate sequence beyond all recognition |