what about the speed on longer seq? Re: [Bioperl-l] regular

[Rob Edwards]

There is also a module I wrote  a while back to go into Bio::Tools that 
will find direct and indirect, exact and some imperfect repeats. I have 
not benchmarked this against other sequences, it does what I need and 
slow is not always bad (it gives you time for coffee...)

You can pass in a sequence object and get back a sequence object with 
the repeats annotated in (so that you can just write them out or get 
their sequences or other bioperly kinds of things).

There is one dependency on Tie::RefHash.

YMMV, but take a look: http://salmonella.org/bioperl/RepeatFinder.pm

Rob