Finding consensus and optimal alignment of circular strings

Title
Finding consensus and optimal alignment of circular strings
Authors
심정섭
Keywords
Consensus strings Circular strings Multiple alignments
Issue Date
2013
Publisher
THEORETICAL COMPUTER SCIENCE
Series/Report no.
THEORETICAL COMPUTER SCIENCE ; Vol468 Startpage 92 Endpage 101
Abstract
Circular strings are different from linear strings in that the last symbol is considered to precede the first symbol. Even though circular strings are biologically important, only a few efforts have been made to solve computational problems on circular strings. In this paper, we introduce consensus problems for circular strings of length n and present the first non-trivial algorithms to find a consensus and an optimal alignment for circular strings by the Hamming distance. They are O(n2 log n)-time algorithms for three circular strings and an O(n3 log n)-time algorithm for four circular strings. Our algorithms are O(n/ log n) times faster than the naive algorithms directly using the solutions for the linear consensus problems, which take O(n3) time for three circular strings and O(n4) time for four circular strings. This speedup was achieved by reducing the problems into correlations and by formulating and solving systems of linear equations. Moreover, our algorithms use only O(n) space.
URI
http://dspace.inha.ac.kr/handle/10505/33494
ISSN
0304-3975
Appears in Collections:
College of Engineering(공과대학) > Computer Engineering (컴퓨터공학) > Journal Papers, Reports(컴퓨터정보공학 논문, 보고서)
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