Formal languages
Reversal-Bounded Multicounter Machines and Their Decision Problems
Journal of the ACM (JACM)
Algebraic and Automata-Theoretic Properties of Formal Languages
Algebraic and Automata-Theoretic Properties of Formal Languages
Implementation of Nondeterministic Finite Automata for Approximate Pattern Matching
WIA '98 Revised Papers from the Third International Workshop on Automata Implementation
The Shortest Common Superstring Problem and Viral Genome Compression
Fundamenta Informaticae - SPECIAL ISSUE ON TRAJECTORIES OF LANGUAGE THEORY Dedicated to the memory of Alexandru Mateescu
Shortest common superstring problem with discrete neural networks
ICANNGA'09 Proceedings of the 9th international conference on Adaptive and natural computing algorithms
DNA'06 Proceedings of the 12th international conference on DNA Computing
The Shortest Common Superstring Problem and Viral Genome Compression
Fundamenta Informaticae - SPECIAL ISSUE ON TRAJECTORIES OF LANGUAGE THEORY Dedicated to the memory of Alexandru Mateescu
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The smallest known biological organisms are, by far, the viruses. One of the unique adaptations that many viruses have aquired is the compression of the genes in their genomes. In this paper we study a formalized model of gene compression in viruses. Specifically, we define a set of constraints that describe viral gene compression strategies and investigate the properties of these constraints from the point of view of genomes as languages. We pay special attention to the finite case (representing real viral genomes) and describe a metric for measuring the level of compression in a real viral genome. An efficient algorithm for establishing this metric is given along with applications to real genomes including automated classification of viruses and prediction of horizontal gene transfer between host and virus.