{"type":"ScholarlyArticle","title":"The DNA Word Design Problem: A New Constraint Model and New Results","authors":[{"name":"Michael Codish","slug":"michael-codish","given":"Michael","family":"Codish","affiliation":"University of the Negev"},{"name":"Michael Frank","slug":"michael-frank","given":"Michael","family":"Frank","affiliation":"University of the Negev"},{"name":"Vitaly Lagoon","slug":"vitaly-lagoon","given":"Vitaly","family":"Lagoon","affiliation":"Cadence Design Systems , USA"}],"abstract":"A fundamental problem in coding theory concerns the computation of\r\n  the maximum cardinality of a set S of length\r\n  n code words over an alphabet of size q, such that every pair of\r\n  code words has Hamming distance at least d, and the set of\r\n  additional constraints U on S is satisfied.  This problem has\r\n  application in several areas, one of which is the design of DNA\r\n  codes where q=4 and the alphabet is {A,C,G,T}.\r\n  We describe a new constraint model for this problem and demonstrate\r\n  that it improves on previous solutions (computes better lower\r\n  bounds) for various instances of the problem.  Our approach is based\r\n  on a clustering of DNA words into small sets of words.  Solutions\r\n  are then obtained as the union of such clusters.  Our approach is\r\n  SAT based: we specify constraints on clusters of DNA words and solve\r\n  these using a Boolean satisfiability solver.","doi":"10.24963/ijcai.2017/82","url":"https://ijcai.org/proceedings/2017/82","pdf":"https://ijcai.org/proceedings/2017/0082.pdf","markdown":"https://ijcai.org/proceedings/2017/82.md","bibtex":"https://ijcai.org/proceedings/2017/bibtex/82","volume":{"slug":"2017","title":"Proceedings of the Twenty-Sixth International Joint Conference on Artificial Intelligence","short_title":"IJCAI 2017","url":"https://ijcai.org/proceedings/2017/","year":2017,"location":"Melbourne, Australia","dates":"19-25 August 2017","editors":"Carles Sierra","isbn":"978-0-9992411-0-3","publisher":"International Joint Conferences on Artificial Intelligence Organization","doi_prefix":"10.24963/ijcai.2017"},"section":"Constraints and Satisfiability","track":"Main track","number":82,"pages":{"first":585,"last":591},"keywords":["Constraints and Satisfiability: Constraints and Satisfiability","Constraints and Satisfiability: Constraint Satisfaction","Multidisciplinary Topics and Applications: Computational Biology and e-Health"],"videos":[],"references":[{"position":1,"raw":"[Adleman, 1994] Leonard M. 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