msbar

Function

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:

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 armed forces.

Usage

Command line arguments


Input file format

msbar reads any sequence USA.

Output file format

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.

Author(s)

History

Target users

Comments