A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems

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.