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EMBOSS: msbar |
It can act on the following sizes of sequence:
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.
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 armies.
% 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 (* if not always prompted): [-sequence] seqall Sequence database USA [-outseq] seqoutall Output sequence(s) USA -count integer Number of times to perform the mutation operations -point list Types of point mutations to perform * -codon list Types of codon mutations to perform. These are only done if the sequence is nucleic. -block list Types of block mutations to perform Optional qualifiers (* if not always prompted): * -inframe bool 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 |
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 | ||||||||||||||
-count | Number of times to perform the mutation operations | Integer 0 or more | 1 | ||||||||||||||
-point | Types of point mutations to perform |
|
0 | ||||||||||||||
-codon | Types of codon mutations to perform. These are only done if the sequence is nucleic. |
|
0 | ||||||||||||||
-block | Types of block mutations to perform |
|
0 | ||||||||||||||
Optional qualifiers | Allowed values | Default | |||||||||||||||
-inframe | Do 'codon' and 'block' operations in frame | 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 |
Program name | Description |
---|---|
shuffleseq | Shuffles a set of sequences maintaining composition |