RNAsnoop is a tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence. RNAsnoop implements a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions in an efficient scanning variant. Complemented by an support vector machine (SVM)-based machine learning approach to distinguish true binding sites from spurious solutions and a system to evaluate comparative information, it presents an efficient and reliable tool for the prediction of H/ACA snoRNA target sites. We apply RNAsnoop to identify the snoRNAs that are responsible for several of the remaining ‘orphan’ pseudouridine modifications in human rRNAs, and we assign a target to one of the five orphan H/ACA snoRNAs in Drosophila.
- Vienna RNA package
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Bioinformatics. 2010 Mar 1;26(5):610-6. Epub 2009 Dec 16.
RNAsnoop: efficient target prediction for H/ACA snoRNAs.
Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF.