TY - GEN

T1 - Consensus optimizing both distance sum and radius

AU - Amir, Amihood

AU - Landau, Gad M.

AU - Na, Joong Chae

AU - Park, Heejin

AU - Park, Kunsoo

AU - Sim, Jeong Seop

PY - 2009

Y1 - 2009

N2 - The consensus string problem is finding a representative string (consensus) of a given set of strings. In this paper we deal with the consensus string problems optimizing both distance sum and radius, where the distance sum is the sum of (Hamming) distances from the strings in to the consensus and the radius is the longest (Hamming) distance from the strings in to the consensus. Although there have been results considering either distance sum or radius, there have been no results considering both as far as we know. We present two algorithms to solve the consensus string problems optimizing both distance sum and radius for three strings. The first algorithm finds the optimal consensus string that minimizes both distance sum and radius, and the second algorithm finds the bounded consensus string such that, given constants s and r, the distance sum is at most s and the radius is at most r. Both algorithms take linear time.

AB - The consensus string problem is finding a representative string (consensus) of a given set of strings. In this paper we deal with the consensus string problems optimizing both distance sum and radius, where the distance sum is the sum of (Hamming) distances from the strings in to the consensus and the radius is the longest (Hamming) distance from the strings in to the consensus. Although there have been results considering either distance sum or radius, there have been no results considering both as far as we know. We present two algorithms to solve the consensus string problems optimizing both distance sum and radius for three strings. The first algorithm finds the optimal consensus string that minimizes both distance sum and radius, and the second algorithm finds the bounded consensus string such that, given constants s and r, the distance sum is at most s and the radius is at most r. Both algorithms take linear time.

UR - http://www.scopus.com/inward/record.url?scp=70350637476&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-03784-9_23

DO - 10.1007/978-3-642-03784-9_23

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AN - SCOPUS:70350637476

SN - 3642037836

SN - 9783642037832

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 234

EP - 242

BT - String Processing and Information Retrieval - 16th International Symposium, SPIRE 2009, Proceedings

T2 - 16th International Symposium on String Processing and Information Retrieval, SPIRE 2009

Y2 - 25 August 2009 through 27 August 2009

ER -