I am trying to find documentation (a paper) on algorithms for Stem Loop
detection. Especially for detection in long sequences (in our case
whole mitochondrial genomes ~17kbp). I have searched in the usual
places (scholar.google.com, pubmed) but I only find algorithms for
secondary RNA structure detection which, in most cases, are
computationally intensive and not suitable for large sequences.
I also know that GCG has stem loop detection. Does anyone know if the
implemented algorithm is suited for long sequences (again ~17kbp)?