|   | msbar | 
Please help by correcting and extending the Wiki pages.
This program changes a sequence, attempting to emulate various forms of mutation. It reads one or more sequences and writes an output file with with a set of (mutated) sequences. The number, size and type of mutation may be specified.
This asks for 5 mutations, with point mutations as changes (substitutions), and the codon and block mutations ignored.
| 
% msbar 
Mutate a sequence
Input sequence(s): tembl:j01636
Number of times to perform the mutation operations [1]: 5
Point mutation operations
         0 : None
         1 : Any of the following
         2 : Insertions
         3 : Deletions
         4 : Changes
         5 : Duplications
         6 : Moves
Types of point mutations to perform [0]: 4
Block mutation operations
         0 : None
         1 : Any of the following
         2 : Insertions
         3 : Deletions
         4 : Changes
         5 : Duplications
         6 : Moves
Types of block mutations to perform [0]: 
Codon mutation operations
         0 : None
         1 : Any of the following
         2 : Insertions
         3 : Deletions
         4 : Changes
         5 : Duplications
         6 : Moves
Types of codon mutations to perform [0]: 
output sequence(s) [j01636.fasta]: 
 | 
Go to the input files for this example
Go to the output files for this example
| 
Mutate a sequence
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -count              integer    [1] Number of times to perform the mutation
                                  operations (Integer 0 or more)
   -point              menu       [0] Types of point mutations to perform
                                  (Values: 0 (None); 1 (Any of the following);
                                  2 (Insertions); 3 (Deletions); 4 (Changes);
                                  5 (Duplications); 6 (Moves))
   -block              menu       [0] Types of block mutations to perform
                                  (Values: 0 (None); 1 (Any of the following);
                                  2 (Insertions); 3 (Deletions); 4 (Changes);
                                  5 (Duplications); 6 (Moves))
*  -codon              menu       [0] Types of codon mutations to perform.
                                  These are only done if the sequence is
                                  nucleic. (Values: 0 (None); 1 (Any of the
                                  following); 2 (Insertions); 3 (Deletions); 4
                                  (Changes); 5 (Duplications); 6 (Moves))
  [-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 | ||||||||||||||
| -count | integer | Number of times to perform the mutation operations | Integer 0 or more | 1 | ||||||||||||||
| -point | list | Types of point mutations to perform | 
 | 0 | ||||||||||||||
| -block | list | Types of block mutations to perform | 
 | 0 | ||||||||||||||
| -codon | list | Types of codon mutations to perform. These are only done if the sequence is nucleic. | 
 | 0 | ||||||||||||||
| [-outseq] (Parameter 2) | seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format | ||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||
| -inframe | boolean | Do 'codon' and 'block' operations in frame | Boolean value Yes/No | No | ||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||
| -othersequence | seqall | If you require that the resulting mutated sequence should not match a set of other sequences, then you can specify that set of sequences here. For example, if you require that the mutated sequence should not be the same as the input sequence, enter the input sequence here. If you want the result to be different to previous results of this program, specify the previous result sequences here. The program will check that the result does not match the sequences specified here before writing it out. If a match is found, then the mutation is started again with a fresh copy of the input sequence. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message. | Readable sequence(s) | asis:N | ||||||||||||||
| -minimum | integer | Minimum size for a block mutation | Integer 0 or more | 1 | ||||||||||||||
| -maximum | integer | Maximum size for a block mutation | Any integer value | 10 | ||||||||||||||
| 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 | ||||||||||||||
| -scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N | ||||||||||||||
| -squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N | ||||||||||||||
| -sformat1 -sformat_sequence | string | Input sequence format | Any string | |||||||||||||||
| -iquery1 -iquery_sequence | string | Input query fields or ID list | Any string | |||||||||||||||
| -ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0 | ||||||||||||||
| -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 | |||||||||||||||
| "-othersequence" associated seqall qualifiers | ||||||||||||||||||
| -sbegin | integer | Start of each sequence to be used | Any integer value | 0 | ||||||||||||||
| -send | integer | End of each sequence to be used | Any integer value | 0 | ||||||||||||||
| -sreverse | boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||||
| -sask | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||||
| -snucleotide | boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||||
| -sprotein | boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||||
| -slower | boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||||
| -supper | boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||||
| -scircular | boolean | Sequence is circular | Boolean value Yes/No | N | ||||||||||||||
| -squick | boolean | Read id and sequence only | Boolean value Yes/No | N | ||||||||||||||
| -sformat | string | Input sequence format | Any string | |||||||||||||||
| -iquery | string | Input query fields or ID list | Any string | |||||||||||||||
| -ioffset | integer | Input start position offset | Any integer value | 0 | ||||||||||||||
| -sdbname | string | Database name | Any string | |||||||||||||||
| -sid | string | Entryname | Any string | |||||||||||||||
| -ufo | string | UFO features | Any string | |||||||||||||||
| -fformat | string | Features format | Any string | |||||||||||||||
| -fopenfile | 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   J01636; SV 1; linear; genomic DNA; STD; PRO; 7477 BP.
XX
AC   J01636; J01637; K01483; K01793;
XX
DT   30-NOV-1990 (Rel. 26, Created)
DT   09-SEP-2004 (Rel. 81, Last updated, Version 8)
XX
DE   E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
XX
KW   acetyltransferase; beta-D-galactosidase; galactosidase; lac operon;
KW   lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene;
KW   lacZ gene; mutagenesis; palindrome; promoter region;
KW   thiogalactoside acetyltransferase.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1243-1266
RX   DOI; 10.1073/pnas.70.12.3581.
RX   PUBMED; 4587255.
RA   Gilbert W., Maxam A.;
RT   "The nucleotide sequence of the lac operator";
RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3581-3584(1973).
XX
RN   [2]
RP   1246-1308
RX   DOI; 10.1073/pnas.70.12.3585.
RX   PUBMED; 4587256.
RA   Maizels N.M.;
RT   "The nucleotide sequence of the lactose messenger ribonucleic acid
RT   transcribed from the UV5 promoter mutant of Escherichia coli";
RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3585-3589(1973).
XX
RN   [3]
RX   PUBMED; 4598642.
RA   Gilbert W., Maizels N., Maxam A.;
RT   "Sequences of controlling regions of the lactose operon";
RL   Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974).
XX
RN   [4]
RA   Gilbert W., Gralla J., Majors A.J., Maxam A.;
RT   "Lactose operator sequences and the action of lac repressor";
RL   (in) Sund H., Blauer G. (Eds.);
RL   PROTEIN-LIGAND INTERACTIONS:193-207;
RL   Walter de Gruyter, New York (1975)
XX
RN   [5]
RP   1146-1282
  [Part of this file has been deleted for brevity]
     cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg      4560
     ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg      4620
     ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct      4680
     ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg      4740
     gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga      4800
     aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct      4860
     gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct      4920
     ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg      4980
     cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta      5040
     agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg      5100
     gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct      5160
     ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac      5220
     ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg      5280
     ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct      5340
     cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg      5400
     tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc      5460
     tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca      5520
     atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg      5580
     gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc      5640
     gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac      5700
     caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag      5760
     gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt      5820
     taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta      5880
     aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt      5940
     acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg      6000
     atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg      6060
     ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga      6120
     taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca      6180
     tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg      6240
     tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact      6300
     attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg      6360
     ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa      6420
     gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt      6480
     gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc      6540
     atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg      6600
     atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca      6660
     gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac      6720
     accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc      6780
     agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca      6840
     ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg      6900
     tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg      6960
     taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc      7020
     acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac      7080
     caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg      7140
     tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca      7200
     gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca      7260
     ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag      7320
     cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag      7380
     actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc      7440
     cagcccgccc atggtaacca ccggcagagc ggtcgac                               7477
//
 | 
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.
| >J01636 J01636.1 E.coli lactose operon with lacI, lacZ, lacY and lacA genes. gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt caattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggt gtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacg cgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaa caactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcac gcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtg gtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatctt ctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccatt gctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagaca cccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctg gtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcg cgtctgcgtctggctggctggcataaatTtctcactcgcaatcaaattcagccgatagcg gaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaat gagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatg cgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgac gataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaacaggattttcgc ctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaag ggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacg caaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcc cgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggc accccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggata acaatttcacacaggaaacagctatgaccatgattacggattcactggccgtcgttttac aacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatcccc ctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgc gcagcctgaatggcgaatggcgctttgcctggtttccggcaccagaagcggtgccggaaa gctggctggagtgcgatcttcctgaggccgatactgtcgtcgtcccctcaaactggcaga tgcacggttacgatgcgcccatctacaccaacgtaacctatcccattacggtcaatccgc cgtttgttcccacggagaatccgacgggttgttactcgctcacatttaatgttgatgaaa gctggctacaggaaggccagacgcgaattatttttgatggcgttaactcggcgtttcatc tgtggtgcaacgggcgctgggtcggttacggccaggacagtcgtttgccgtctgaatttg acctgagcgcatttttacgcgccggagaaaaccgcctcgcggtgatggtgctgcgttgga gtgacggcagttatctggaagatcaggatatgtggcggatgagcggcattttccgtgacg tctcgttgctgcataaaccgactacacaaatcagcgatttccatgttgccactcgcttta atgatgatttcagccgcgctgtactggaggctgaagttcagatgtgcggcgagttgcgtg actacctacgggtaacagtttctttatggcagggtgaaacgcaggtcgccagcggcaccg cgcctttcggcggtgaaattatcgatgagcgtggtggttatgccgatcgcgtcacactac gtctgaacgtcgaaaacccgaaactgtggagcgccgaaatcccgaatctctatcgtgcgg tggttgaactgcacaccgccgacggcacgctgattgaagcagaagcctgcgatgtcggtt tccgcgaggtgcggattgaaaatggtctgctgctgctgaacggcaagccgttgctgattc gaggcgttaaccgtcacgagcatcatcctctgcatggtcaggtcatggatgagcagacga tggtgcaggatatcctgctgatgaagcagaacaactttaacgccgtgcgctgttcgcatt atccgaaccatccgctgtggtacacgctgtgcgaccgctacggcctgtatgtggtggatg aagccaatattgaaacccacggcatggtgccaatgaatcgtctgaccgatgatccgcgct ggctaccggcgatgagcgaacgcgtaacgcgaatggtgcagcgcgatcgtaatcacccga gtgtgatcatctggtcgctggggaatgaatcaggccacggcgctaatcacgacgcgctgt atcgctggatcaaatctgtcgatccttcccgcccggtgcagtatgaaggcggcggagccg acaccacggccaccgatattatttgcccgatgtacgcgcgcgtggatgaagaccagccct tcccggctgtgccgaaatggtccatcaaaaaatggctttcgctacctggagagacgcgcc cgctgatcctttgcgaatacgcccacgcgatgggtaacagtcttggcggtttcgctaaat [Part of this file has been deleted for brevity] tgttcggtttattctttttcttttacttttttatcatgggagcctacttcccgtttttcc cgatttggctacatgacatcaaccatatcagcaaaagtgatacgggtattatttttgccg ctatttctctgttctcgctattattccaaccgctgtttggtctgctttctgacaaactcg ggctgcgcaaatacctgctgtggattattaccggcatgttagtgatgtttgcgccgttct ttatttttatcttcgggccactgttacaatacaacattttagtaggatcgattgttggtg gtatttatctaggcttttgttttaacgccggtgcgccagcagtagaggcatttattgaga aagtcagccgtcgcagtaatttcgaatttggtcgcgcgcggatgtttggctgtgttggct gggcgctgtgtgccTcgattgtcggcatcatgttcaccatcaataatcagtttgttttct ggctgggctctggctgtgcactcatcctcgccgttttactctttttcgccaaaacggatg cgccctcttctgccacggttgccaatgcggtaggtgccaaccattcggcatttagcctta agctggcactggaactgttcagacagccaaaactgtggtttttgtcactgtatgttattg gcgtttcctgcacctacgatgtttttgaccaacagtttgctaatttctttacttcgttct ttgctaccggtgaacagggtacgcgggtatttggctacgtaacgacaatgggcgaattac ttaacgcctcgattatgttctttgcgccactgatcattaatcgcatcggtgggaaaaacg ccctgctgctggctggcactattatgtctgtacgtattattggctcatcgttcgccacct cagcgctggaagtggttattctgaaaacgctgcatatgtttgaagtaccgttcctgctgg tgggctgctttaaatatattaccagccagtttgaagtgcgtttttcagcgacgatttatc tggtctgtttctgcttctttaagcaactggcgatgatttttatgtctgtactggcgggca atatgtatgaaagcatcggtttccagggcgcttatctggtgctgggtctggtggcgctgg gcttcaccttaatttccgtgttcacgcttagcggccccggcccgctttccctgctgcgtc gtcaggtgaatgaagtcgcttaagcaatcaatgtcggatgcggcgcgacgcttatccgac caacatatcataacggagtgatcgcattgaacatgccaatgaccgaaagaataagagcag gcaagctatttaccgatatgtgcgaaggcttaccggaaaaaagacttcgtgggaaaacgt taatgtatgagtCtaatcactcgcatccatcagaagttgaaaaaagagaaagcctgatta aagaaatgtttgccacggtaggggaaaacgcctgggCagaaccgcctgtctatttctctt acggttccaacatccatataggccgcaatttttatgcaaatttcaatttaaccattgtcg atgactacacggtaacaatcggtgataacgtactgattgcacccaacgttactctttccg ttacgggacaccctgtacaccatgaattgagaaaaaacggcgagatgtactcttttccga taacgattggcaataacgtctggatcggaagtcatgtggttattaatccaggcgtcacca tcggggataattctgttattggcgcgggtagtatcgtcacaaaagacattccaccaaacg tcgtggcggctggcgttccttgtcgggttattcgcgaaataaacgaccgggataagcact attatttcaaagattataaagttgaatcgtcagtttaaattataaaaattgcctgatacg ctgcgcttatcaggcctacaagttcagcgatctacattagccgcatccggcatgaacaaa gcgcaggaacaagcgtcgcatcatgcctctttgacccacagctgcggaaaacgtactggt gcaaaacgcagggttatgatcatcagcccaacgacgcacagcgcatgaaatgcccagtcc atcaggtaattgccgctgatactacgcagcacgccagaaaaccacggggcaagcccggcg atgataaaaccgattccctgcataaacgccaccagcttgccagcaatagccggttgcaca gagtgatcgagcgccagcagcaaacagagcggaaacgcgccgcccagacctaacccacac accatcgcccacaataccggcaattgcatcggcagccagataaagccgcagaaccccacc agttgtaacaccagcgccagcattaacagtttgcgccgatcctgatggcgagccatagca ggcatcagcaaagctcctgcggcttgcccaagcgtcatcaatgccagtaaggaaccgctg tactgcgcgctggcaccaatctcaatatagaaagcgggtaaccaggcaatcaggctggcg taaccgccgttaatcagaccgaagtaaacacccagcgtccacgcgcggggagtgaatacc acgcgaaccggagtggttgttgtcttgtgggaagaggcgacctcgcgggcgctttgccac caccaggcaaagagcgcaacaacggcaggcagcgccaccaggcgagtgtttgataccagg tttcgctatgttgaactaaccagggcgttatggcggcaccaagcccaccgccgcccatca gagccgcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtttaatca ccgaagcatcaccgcctgaatgatgccgatccccaccccaccaagcagtgcgctgctaag cagcagcgcactttgcgggtaaagctcacgcatcaatgcaccgacggcaatcagcaacag actgatggcgacactgcgacgttcgctgacatgctgatgaagccagcttccggccagcgc cagcccgcccatggtaaccaccggcagagcggtcgac | 
The output is a sequence file with 5 substitutions relative to the original sequence.
The qualifiers allow the number, size and type of mutation to be controlled.
The "size" of mutation may be set as following:
If the sequence is nucleic, the codon and block-sized operations can optionally be done in-frame. This causes the minimum block size to be set to 3 and the randomly chosen positions to be multiples of 3.
For each of the above size of sequence it can produce the effects of any of the following types of mutation at a randomly chosen position:
The input and output sequences may not differ if only a few changes are chosen as (for example) one in four nucleic acid point substitutions will not change the sequence.
There is no selection of the types of mutation to produce viable sequence as there would be in a real organism. In particular, there is no attempt to bias mutations of nucleic acid sequences to conform to the C+G ratio in the sequence or to bias the codons in the direction of the frequencies used in the organism. This program emulates mutation, not selection.
This program was named from the acronym of "Mutate Sequence Beyond All Recognition", by analogy with the acronym "fubar" commonly used in the US and UK armed forces.
If you require the mutated sequences to not match some other set of sequences, this set may be specified with the -othersequence qualifier. For example, the mutants should not match the input sequence, or the results of a previous run of this program. msbar ensures the mutants do not match the specified sequences. If a match is found, then the mutation is started again with a fresh copy of the input sequence. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message.
| Program name | Description | 
|---|---|
| shuffleseq | Shuffle a set of sequences maintaining composition | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.