A1 Refereed original research article in a scientific journal
Parallelism in gene assembly
Authors: Harju T, Li C, Petre I, Rozenberg G
Publication year: 2005
Journal:: Lecture Notes in Computer Science
Journal name in source: DNA COMPUTING
Journal acronym: LECT NOTES COMPUT SC
Volume: 3384
First page : 138
Last page: 148
Number of pages: 11
ISBN: 3-540-26174-5
ISSN: 0302-9743
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 (Id, 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.
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 (Id, 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.
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