Gesellschaft fr Informatik e.V.

Lecture Notes in Informatics

German Conference on Bioinformatics P-83, 93-102 (2006).

Gesellschaft für Informatik, Bonn

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Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs

Axel Mosig , Ivo L. Hofacker and Peter F. Stadler


The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules such as bacterial genomes since in practice all analysis is performed in sequence windows, this is not true for viroids and related sequences which are usually only a few hundred basepairs long. In this contribution we present basic algorithms and corresponding software for circular RNAs. In particular, we discuss the problem of pairwise and multiple cyclic sequence alignments with affine gap costs, and an extension of a recent approach to circular RNA folding to the computation of consensus structures.

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Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-177-5

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