Publications - Published papers

Please find below publications of our group. Currently, we list 501 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems

Will, Sebastian and Stadler, Peter F.

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Lecture Notes in Computer Science Volume 8701, 2014, pp 135-147

Abstract


Circularized RNAs have received considerable attention is the last few years following the discovery that they are not only a rather common phenomenon in the transcriptomes of Eukarya and Archaea but also may have key regulatory functions. This calls for the adaptation of basic tools of sequence analysis to accommodate cyclic sequences. Here we discuss a common formal framework for linear and circular alignments as partitions that preserve (cyclic) order. We focus on the similarities and differences and describe a prototypical ILP formulation.

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