Approximations and partial solutions for the consensus sequence problem

Amihood Amir, Haim Paryenty, Liam Roditty

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

7 Scopus citations

Abstract

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.

Original languageEnglish
Title of host publicationString Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings
Pages168-173
Number of pages6
DOIs
StatePublished - 2011
Event18th International Symposium on String Processing and Information Retrieval, SPIRE 2011 - Pisa, Italy
Duration: 17 Oct 201121 Oct 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7024 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference18th International Symposium on String Processing and Information Retrieval, SPIRE 2011
Country/TerritoryItaly
CityPisa
Period17/10/1121/10/11

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