I am searching for RNA stems of approx. 10 to 1000 bases. Is there a fast, BLAST-like tool for scanning DNA sequences of, for instance, 10kB?
As I want to extend this method to whole genome searches, exact algorithms are too much time consuming. I am only looking for sequence similarity. Energy values such as MFE should not taken into account. Unfortunately, BLAST lacks the ability to detect the uracil wobble pairs. Thus, very short stems are undetectable.
Is there any alignment tool I can use?