An inversion and a translocation are important in bio sequence analysis and motivate researchers to consider the sequence alignment problem using these operations. Based on inversion and translocation, we introduce a new alignment problem with non-overlapping inversions and translocations-given two strings x and y, find an alignment with non-overlapping inversions and translocations for x and y. This problem has interesting application for finding a common sequence from two mutated sequences. We, in particular, consider the alignment problem when non-overlapping inversions and translocations are allowed for both x and y. We design an efficient algorithm that determines the existence of such an alignment and retrieves an alignment, if exists.
Bibliographical noteFunding Information:
We wish to thank the referees for the careful reading of the paper and many valuable suggestions. This research was supported by the Basic Science Research Program through NRF (National Research Foundation) of Korea funded by MEST ( 2012R1A1A2044562 ). Kim was supported by NRF Grant funded by the Korean Government ( NRF-2013-Global Ph.D. Fellowship Program ).
© 2014 Elsevier B.V.
All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)