MSBARP

Mutate sequence beyond all recognition

This program changes a sequence a lot or a little, attempting to emulatevarious 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 canoptionally be done in-frame. This causes the minimum block size to beset 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 anyof 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 arechosen as (for example) one in four nucleic acid point substitutionswill not change the sequence.

N.B. There is no selection of the types of mutation to produce viablesequence as there would be in a real organism. In particular, there isno attempt to bias mutations of nucleic acid sequences to conform to theC+G ratio in the sequence or to bias the codons in the direction of thefrequencies used in the organism. This program emulates mutation, notselection.

This program was named from the acronym of "Mutate Sequence Beyond AllRecognition", by analogy with the acronym "fubar" commonly used in theUS and UK armed forces.