| msbar

## Function

Mutate sequence beyond all recognition

## Description

This program changes a sequence a lot or a little, attempting to emulate various forms of mutation. You can set the number and types of mutations.

It can act on the following sizes of sequence:

- 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.

N.B. 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.

## 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 sequence beyond all recognition
    Input sequence(s): tembl:eclac
    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 [eclac.fasta]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-sequence]          seqall     Sequence database USA
       -count              integer    Number of times to perform the mutation
                                      operations
       -point              menu       Types of point mutations to perform
       -block              menu       Types of block mutations to perform
    *  -codon              menu       Types of codon mutations to perform. These
                                      are only done if the sequence is nucleic.
      [-outseq]            seqoutall  Output sequence(s) USA

       Optional qualifiers (* if not always prompted):
    *  -inframe            boolean    Do 'codon' and 'block' operations in frame

       Advanced qualifiers:
       -minimum            integer    Minimum size for a block mutation
       -maximum            integer    Maximum size for a block mutation
       -other              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.

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-other" related qualifiers
       -sbegin              integer    First base used
       -send                integer    Last base used, def=seq length
       -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
       -sopenfile           string     Input filename
       -sdbname             string     Database name
       -sid                 string     Entryname
       -ufo                 string     UFO features
       -fformat             string     Features format
       -fopenfile           string     Features file name
      "-outseq" related 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 standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. 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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
-count | Number of times to perform the mutation operations | Integer 0 or more | 1
-point | Types of point mutations to perform |
0 | (None)
1 | (Any of the following)
2 | (Insertions)
3 | (Deletions)
4 | (Changes)
5 | (Duplications)
6 | (Moves)
| 0
-block | Types of block mutations to perform |
0 | (None)
1 | (Any of the following)
2 | (Insertions)
3 | (Deletions)
4 | (Changes)
5 | (Duplications)
6 | (Moves)
| 0
-codon | Types of codon mutations to perform. These are only done if the sequence is nucleic. |
0 | (None)
1 | (Any of the following)
2 | (Insertions)
3 | (Deletions)
4 | (Changes)
5 | (Duplications)
6 | (Moves)
| 0
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
Optional qualifiers | Allowed values | Default
-inframe | Do 'codon' and 'block' operations in frame | Boolean value Yes/No | No
Advanced qualifiers | Allowed values | Default
-minimum | Minimum size for a block mutation | Integer 0 or more | 1
-maximum | Maximum size for a block mutation | Any integer value | 10
-other | 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

## Input file format

msbar reads any sequence USA.

### Input files for usage example

'tembl:eclac' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:eclac

    ID   ECLAC      standard; DNA; PRO; 7477 BP.
    XX
    AC   J01636; J01637; K01483; K01793;
    XX
    SV   J01636.1
    XX
    DT   30-NOV-1990 (Rel. 26, Created)
    DT   04-MAR-2000 (Rel. 63, Last updated, Version 7)
    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; gamma subdivision; Enterobacteriaceae;
    OC   Escherichia.
    XX
    RN   [1]
    RP   1243-1266
    RX   MEDLINE; 74055539.
    RA   Gilbert W., Maxam A.;
    RT   "The nucleotide sequence of the lac operator";
    RL   Proc. Natl. Acad. Sci. U.S.A. 70:3581-3584(1973).
    XX
    RN   [2]
    RP   1246-1308
    RX   MEDLINE; 74055540.
    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. 70:3585-3589(1973).
    XX
    RN   [3]
    RX   MEDLINE; 74174501.
    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

### Output files for usage example

### File: eclac.fasta

    >ECLAC J01636.1 E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
    gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt
    caattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggt
    gtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacg
    cgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaa
    caactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcac
    gcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtg
    gtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatctt
    ctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccatt
    gctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagaca
    cccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctg
    gtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcg
    cgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcg
    gaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaat
    gagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatg
    cgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgac
    gataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaacaggattttcgc
    ctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaag
    ggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacg
    caaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcc
    cgactggaaagcgggcagtgagcgcaacgcaattaaGgtgagttagctcactcattaggc
    accccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggata
    acaatttcacacaggaaacagctatgaccatgattacggattcactggccgAcgttttac
    aacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatcccc
    ctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgc
    gcagcctgaatggcgaatggcgctttgcctggtttccggcaccagaagcggtgccggaaa
    gctggctggagtgcgatcttcctgaggccgatactgtcgtcgtcccctcaaactggcaga
    tgcacggttacgatgcgcccatctacaccaacgtaacctatcccattacggtcaatccgc
    cgtttgttcccacggagaatccgacgggttgttactcgctcacatttaatgttgatgaaa
    gctggctacaggaaggccagacgcgaattatttttgatggcgttaactcggcgtttcatc
    tgtggtgcaacgggcgctgggtcggttacggccaggacagtcgtttgccgtctgaatttg
    acctgagcgcatttttacgcgccggagaaaaccgcctcgcggtgatggtgctgcgttgga
    gtgacggcagttatctggaagatcaggatatgtggcggatgagcggcattttccgtgacg
    tctcgttgctgcataaaccgactacacaaatcagcgatttccatgttgccactcgcttta
    atgatgatttcagccgcgctgtactggaggctgaagttcagatgtgcggcgagttgcgtg
    actacctacgggtaacagtttctttatggcagggtgaaacgcaggtcgccagcggcaccg
    cgcctttcgTcggtgaaattatcgatgagcgtggtggttatgccgatcgcgtcacactac
    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
    cgccctcttctgccacggttgccaatgcggtaggtgccaaccattcggcGtttagcctta
    agctggcactggaactgttcagacagccaaaactgtggtttttgtcactgtatgttattg
    gcgtttcctgcacctacgatgtttttgaccaacagtttgctaatttctttacttcgttct
    ttgctaccggtgaacagggtacgcgggtatttggctacgtaacgacaatgggcgaattac
    ttaacgcctcgattatgttctttgcgccactgatcattaatcgcatcggtgggaaaaacg
    ccctgctgctggctggcactattatgtctgtacgtattattggctcatcgttcgccacct
    cagcgctggaagtggttattctgaaaacgctgcatatgtttgaagtaccgttcctgctgg
    tgggctgctttaaatatattaccagccagtttgaagtgcgtttttcagcgacgatttatc
    tggtctgtttctgcttctttaagcaactggcgatgatttttatgtctgtactggcgggca
    atatgtatgaaagcatcggtttccagggcgcttatctggtgctgggtctggtggcgctgg
    gcttcaccttaatttccgtgttcacgcttagcggccccggcccgctttccctgctgcgtc
    gtcaggtgaatgaagtcgcttaagcaatcaatgtcggatgcggcgcgacgcttatccgac
    caacatatcataacggagtgatcgcattgaacatgccaatgaccgaaagaataagagcag
    gcaagctatttaccgatatgtgcgaaggcttaccggaaaaaagacttcgtgggaaaacgt
    taatgtatgagtttaatcactcgcatccatcagaagttgaaaaaagagaaagcctgatta
    aagaaatgtttgccacggtaggggaaaacgcctgggtagaaccgcctgtctatttctctt
    acggttccaacatccatataggccgcaatttttatgcaaatttcaatttaaccattgtcg
    atgactacacggtaacaatcggtgataacgtactgattgcacccaacgttactctttccg
    ttacgggacaccctgtacaccatgaattgagaaaaaacggcgagatgtactcttttccga
    taacgattggcaataacgtctggatcggaagtcatgtggttattaatccaggcgtcacca
    tcggggataattctgttattggcgcgggtagtatcgtcacaaaagacattccaccaaacg
    tcgtggcggctggcgttccttgtcgggttattcgcgaaataaacgaccgggataagcact
    attatttcaaagattataaagttgaatcgtcagtttaaattataaaaattgcctgatacg
    ctgcgcttatcaggcctacaagttcagcgatctacattagccgcatccggcatgaacaaa
    gcgcaggaacaagcgtcgcatcatgTctctttgacccacagctgcggaaaacgtactggt
    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

None.

## 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 (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## 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