PUB - Publikationen an der Universität Bielefeld

This thesis describes a new method to calculate pairwise alignments of RNA sequences of which both the primary sequence and the secondary structure are known. Thus, sequences can be aligned like tRNAs, 5s-rRNAs, RNAseP molecules, 16s-rRNAs, 18s-rRNAs, 23s-rRNAs and so on. That is, in this thesis the focus is set to calculate an alignment between relatively similar RNA sequences. This means that sometimes no alignment is calculated at all if the structure of two sequences is too different. However, there are two major benefits of the new method. One is that both the primary sequence and the secondary structure are taken into account. The second is that the method works very fast: an alignment between two sequences S and P is calculated in averige case in O((n+m) log (n+m)), where n and m represent the length of S and P. Thus, even pairwise alignments between 28s-rRNAs are calculated very fast. The method depends on a sequence cutting up, an adopted alphabet and the well known standard edit distance approach. Tertiary structural elements are not taken into account.