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 -