Summary
RNAsnoop is a tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence. You can get it from here. Perlscripts to filter the RNAsnoop output are here . Finally a pdf-formated short tutorial on RNAsnoop as well as the accompanying example sequences are located here A similar program for C/D snoRNAs can be found here