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,