@inproceedings{7c125b049e4c4ceaaef5b8d9aeab1c09,
title = "A common framework for linear and cyclic multiple sequence alignment problems",
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 = "circular RNAs, cyclic orders, cyclic sequence alignment, integer linear programming, multiple sequence alignment",
author = "Sebastian Will and Stadler, \{Peter F.\}",
year = "2014",
month = jan,
day = "1",
doi = "10.1007/978-3-662-44753-6\_11",
language = "English",
isbn = "9783662447529",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "135--147",
booktitle = "Algorithms in Bioinformatics - 14th International Workshop, WABI 2014, Proceedings",
note = "14th International Workshop on Algorithms in Bioinformatics, WABI 2014 ; Conference date: 08-09-2014 Through 10-09-2014",
}