Parallelism in gene assembly

Authors:
Tero Harju;Chang Li;Ion Petre;Grzegorz Rozenberg
Affiliations:
Department of Mathematics, University of Turku, Turku, Finland;Department of Computer Science, Åbo Akademi University, Turku, Finland;Department of Computer Science, Åbo Akademi University, Turku, Finland;Leiden Institute for Advanced Computer Science, Leiden University, Leiden, The Netherlands
Venue:
DNA'04 Proceedings of the 10th international conference on DNA computing
Year:
2004

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Abstract

The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational point of view, with ciliates even using the linked list data structure. Three molecular operations (ld,hi, and dlad) have been postulated for the gene assembly process. We initiate here the study of parallelism of this process by investigating several natural questions, such as: when can a number of operations be applied in parallel to a gene pattern, or how many steps are needed to assemble in parallel a micronuclear gene. We believe that the study of parallelism contributes to a better understanding of the nature of gene assembly, and in particular it provides a new insight in the complexity of this process.