Publications - Working papers
Please find below working papers of our group. Currently, we list 58 working papers.
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A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problem
Sebastian Will, Peter F. Stadler
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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.
Keywords
cyclic sequence alignment, multiple sequence alignment, cyclic orders, integer linear programming, circular RNAs