Function

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

Command line arguments

Input file format

Output file format

The output is a sequence file with 5 substitutions relative to the original sequence.

Data files

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

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Author(s)

History

Target users

Comments