msbar 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 Mutate a sequence Description 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. Usage Here is a sample session with msbar 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 Command line arguments Mutate a sequence Version: EMBOSS:6.4.0.0 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 [.] Sequence set(s) filename and optional format (output USA) Additional (Optional) qualifiers (* if not always prompted): * -inframe boolean [N] Do 'codon' and 'block' operations in frame Advanced (Unprompted) qualifiers: -othersequence seqall [asis:N] 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. -minimum integer [1] Minimum size for a block mutation (Integer 0 or more) -maximum integer [10] Maximum size for a block mutation (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 "-othersequence" associated qualifiers -sbegin integer Start of each sequence to be used -send integer End of each sequence to be used -sreverse boolean Reverse (if DNA) -sask boolean Ask for begin/end/reverse -snucleotide boolean Sequence is nucleotide -sprotein boolean Sequence is protein -slower boolean Make lower case -supper boolean Make upper case -sformat string Input sequence format -sdbname string Database name -sid string Entryname -ufo string UFO features -fformat string Features format -fopenfile 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 msbar 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:j01636' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:j01636 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 // 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: j01636.fasta >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. Data files None. Notes The qualifiers allow the number, size and type of mutation to be controlled. The "size" of mutation may be set as following: * Point (single base or residue change) * Codon (not applicable in proteins) * Block of sequence (of a specified minimum and maximum random size) 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: * Insertion of a randomly generated sequence * Deletion * Change (deletion then insertion of a random sequence of the same size) * Duplication at an adjacent position * Move region from one position to another (without deletion of the original) * Any of the above, chosen at random. * None of the above 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. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with a status of 0. Known bugs None. See also Program name Description shuffleseq Shuffles a set of sequences maintaining composition Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (1999) - Gary Williams Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None