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Parallelism in Gene Assemby

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg, Parallelism in Gene Assemby. In: Claudio Ferretti, Giancarlo Mauri, Claudio Zandron (Eds.), Proceedings of the 10th International Meeting on DNA Computing, DNA 10, Lecture Notes in Computer Science, 140–150, Springer, 2005.

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
($\mld,\mhi$, and $\mdlad$) 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.

BibTeX entry:

@INPROCEEDINGS{inpHaLiPeRo05a,
  title = {Parallelism in Gene Assemby},
  booktitle = {Proceedings of the 10th International Meeting on DNA Computing, DNA 10},
  author = {Harju, Tero and Li, Chang and Petre, Ion and Rozenberg, Grzegorz},
  series = {Lecture Notes in Computer Science},
  editor = {Ferretti, Claudio and Mauri, Giancarlo and Zandron, Claudio},
  publisher = {Springer},
  pages = {140–150},
  year = {2005},
}

Belongs to TUCS Research Unit(s): FUNDIM, Fundamentals of Computing and Discrete Mathematics, Computational Biomodeling Laboratory (Combio Lab)

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