msbar

msbar

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

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 Input sequence: embl:eclaci Output sequence [eclaci.fasta]:  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 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]: 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]:

Mandatory qualifiers (bold 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 (bold 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.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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