TY - GEN

T1 - Approximations and partial solutions for the consensus sequence problem

AU - Amir, Amihood

AU - Paryenty, Haim

AU - Roditty, Liam

PY - 2011

Y1 - 2011

N2 - The problem of finding the consensus of a given set of strings is formally defined as follows: given a set of strings S = {s1,...sk}, and a constant d, find, if it exists, a string s*, such that the Hamming distance of s* from each of the strings does not exceed d. In this paper we study an LP relaxation for the problem. We prove an additive upper bound, depending only in the number of strings k, and randomized bounds. We show that empirical results are much better. We also compare our program with some algorithms reported in the literature, and it is shown to perform well.

AB - The problem of finding the consensus of a given set of strings is formally defined as follows: given a set of strings S = {s1,...sk}, and a constant d, find, if it exists, a string s*, such that the Hamming distance of s* from each of the strings does not exceed d. In this paper we study an LP relaxation for the problem. We prove an additive upper bound, depending only in the number of strings k, and randomized bounds. We show that empirical results are much better. We also compare our program with some algorithms reported in the literature, and it is shown to perform well.

UR - http://www.scopus.com/inward/record.url?scp=80053968442&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-24583-1_17

DO - 10.1007/978-3-642-24583-1_17

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AN - SCOPUS:80053968442

SN - 9783642245824

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

SP - 168

EP - 173

BT - String Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings

T2 - 18th International Symposium on String Processing and Information Retrieval, SPIRE 2011

Y2 - 17 October 2011 through 21 October 2011

ER -