A topological framework for signed permutations

Abstract In this paper, we present a topological framework for studying signed permutations and their reversal distance. This framework is based on a presentation of orientable and non-orientable fatgraphs via sectors. As an application, we give an alternative approach and interpretation of the Hannenhalli–Pevzner formula for the reversal distance of sorting signed permutations. This is obtained by constructing a bijection between signed permutations and certain equivalence classes of fatgraphs, called π -maps. We study the action of reversals and show that they either splice, glue or half-flip external vertices, which implies that any reversal changes the topological genus by at most one. We show that the lower bound of the reversal distance of a signed permutation equals the topological genus of its π -maps. We then discuss how the new topological model connects to other sorting problems.

[1]  Carsten Wiuf,et al.  Fatgraph models of proteins , 2009, 0902.1025.

[2]  E. Westhof,et al.  Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.

[3]  Jens Stoye,et al.  Common intervals and sorting by reversals: a marriage of necessity , 2002, ECCB.

[4]  Christian M. Reidys,et al.  Topology and prediction of RNA pseudoknots , 2011, Bioinform..

[5]  Jiunn-Liang Chen,et al.  Functional analysis of the pseudoknot structure in human telomerase RNA. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Anne Bergeron,et al.  A very elementary presentation of the Hannenhalli-Pevzner theory , 2005, Discret. Appl. Math..

[7]  Alberto Caprara,et al.  Sorting by reversals is difficult , 1997, RECOMB '97.

[8]  Guillaume Chapuy,et al.  Counting unicellular maps on non-orientable surfaces , 2010, Adv. Appl. Math..

[9]  Haim Kaplan,et al.  A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals , 1999, SIAM J. Comput..

[11]  D. W. Staple,et al.  Open access, freely available online Primer Pseudoknots: RNA Structures with Diverse Functions , 2022 .

[12]  Luc Jaeger,et al.  RNA pseudoknots , 1992, Current Biology.

[13]  David Sankoff,et al.  Edit Distance for Genome Comparison Based on Non-local Operations * 1 Role of Rearrangements in Evolution , .

[14]  David Sankoff,et al.  Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement , 1995, Algorithmica.

[15]  David A. Christie,et al.  A 3/2-approximation algorithm for sorting by reversals , 1998, SODA '98.

[16]  Richard Friedberg,et al.  Efficient sorting of genomic permutations by translocation, inversion and block interchange , 2005, Bioinform..

[17]  Pavel A. Pevzner,et al.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals , 1995, JACM.

[18]  A. Zee,et al.  Topological classification of RNA structures. , 2006, Journal of molecular biology.

[19]  David A. Christie,et al.  Sorting Permutations by Block-Interchanges , 1996, Inf. Process. Lett..

[20]  Guillaume Fertin,et al.  Sorting by Transpositions Is Difficult , 2010, SIAM J. Discret. Math..

[21]  Vineet Bafna,et al.  Genome Rearrangements and Sorting by Reversals , 1996, SIAM J. Comput..

[22]  Simon Gog,et al.  Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation , 2008, J. Comput. Biol..

[23]  William S. Massey,et al.  Algebraic Topology: An Introduction , 1977 .

[24]  J. Nadeau,et al.  Lengths of chromosomal segments conserved since divergence of man and mouse. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[25]  David A. Bader,et al.  A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study , 2001, J. Comput. Biol..

[26]  Guillaume Chapuy A new combinatorial identity for unicellular maps, via a direct bijective approach , 2011, Adv. Appl. Math..

[27]  W. Ewens,et al.  The chromosome inversion problem , 1982 .

[28]  A. Zee,et al.  RNA folding and large N matrix theory , 2001, cond-mat/0106359.

[29]  Vineet Bafna,et al.  Sorting by Transpositions , 1998, SIAM J. Discret. Math..

[30]  Haim Kaplan,et al.  Faster and simpler algorithm for sorting signed permutations by reversals , 1997, SODA '97.