[Bioperl-l] [BiO BB] Tool to mutate DNA sequence

[pmr at ebi.ac.uk]

Ryan Golhar writes:

> Does anyone know of tool to mutate a DNA sequence by a specified amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the original.

EMBOSS has the msbar program ("mutate sequence beyond all recognition")
which allows you to select the number and type of changes.

With some tuning of options to match the sequence length you should be
able to get results that match whatever your definition of 75% similar
might be (amazing how much more similarity you can get by adding gaps in
an alignment :-)

If you can specify a clear and generally useful way to define what you
need we could of course add a "percent change" option to the msbar program
for a future release.

Hope that helps,

Peter