search for inverted repeats

[twetjen]

Hi Frank,

you should check out the software REPuter at 
(http://bibiserv.techfak.uni-bielefeld.de/reputer/). I'm not sure how 
the max length of DNA sequences is that it can handle, however, it does 
compute different kinds of repeats.

Greatings,

Tom

Frank O. Fackelmayer wrote:

> Hi all,
> I´m currently thinking about a project based on inverted repeats in
> complete genomes. What I´m looking for is a program that allows
> searching complete genomes (like a blast search), and not only single
> input sequences. Features of the program should be like those of the
> EMBOSS "palindrome" program, where you can set parameters such as
> minimal and maximal length of the repeats (only repeats smaller than
> 30nt per half-site would be interesting), the minimal and maximal
> distance between half-sites (the half-sites must have a spacer between
> them), and the allowed mismatches (only completely complementary
> sequences, i.e. 0 mismatches).
> 
> Does anyone of you have an idea what program(s) could be suited?
> 
> Thank in advance,
> Frank
> ---
> 
>