“One of the oldest forms of life on Earth has been revealed as a natural born computer programmer.”
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 lists data structure. Three molecular operations (ld, hi, and dlad) have been postulated for the gene assembly process. We initiate here the study of parallelism in this process, raising 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. In particular, this gives rise to a new measure of complexity for the process of gene assembly in ciliates.
Similar content being viewed by others
References
A Ehrenfeucht T Harju I Petre DM Prescott G Rozenberg (2003) ArticleTitleFormal systems for gene assembly in ciliates Theoretical Computer Science 292 199–219 Occurrence Handle1964634 Occurrence Handle10.1016/S0304-3975(01)00223-7
Ehrenfeucht A, Harju T, Petre I and Rozenberg G (2002a) Patterns of micronuclear genes in ciliates. In: Jonoska N and Seeman N (eds) Proceedings of the 7th International Conference on DNA-Based Computers, Tampa, FL, USA, June 10–13, 2001, Lecture Notes in Computer Science, 2340, pp. 279–289. Springer
A Ehrenfeucht T Harju I Petre G Rozenberg (2002b) ArticleTitleCharacterizing the micronuclear gene patterns in ciliates Theory of Computing Systems 35 501–519 Occurrence Handle1922074 Occurrence Handle10.1007/s00224-002-1043-9
Ehrenfeucht A, Harju T, Petre I, Prescott DM and Rozenberg G (2004) Computation in Living Cells: Gene Assembly in Ciliates. Springer
A Ehrenfeucht I Petre DM Prescott G Rozenberg (2001a) Universal and simple operations for gene assembly in ciliates V Mitrana C Martin-Vide (Eds) Words, Sequences, Languages: Where Computer Science, Biology and Linguistics Meet Kluwer Academic Dordrecht 329–342
A Ehrenfeucht I Petre DM Prescott G Rozenberg (2001b) ArticleTitleString and graph reduction systems for gene assembly in ciliates Mathematical Structures in Computer Science 12 113–134 Occurrence Handle1900372 Occurrence Handle10.1017/S0960129501003516
A Ehrenfeucht I Petre DM Prescott G Rozenberg (2001c) Circularity and other invariants of gene assembly in ciliates M Ito Gh Păun S Yu (Eds) Words, Semigroups, and Transductions World Scientific Singapore 81–97
A Ehrenfeucht DM Prescott G Rozenberg (2001d) Computational aspects of gene (un)scrambling in ciliates LF Landweber E Winfree (Eds) Evolution as Computation Springer Berlin, Heidelberg, New York 216–256
T Harju I Petre G Rozenberg (2004) Gene assembly in ciliates: formal frameworks G Paun G Rozenberg A Salomaa (Eds) Current Trends in Theoretical Computer Science NumberInSeries1 World Scientific Singapore 543–558
Harju T, Li C, Petre I and Rozenberg G (2005) Parallelism in gene assembly. In: Proceedings of the 10th International Meeting on DNA-based computers DNA 10, Milan, Italy, Lecture Notes in Computer Science, 3384, 2005, pp. 140–150. Springer, Berlin
CL Jahn LA Klobutcher (2000) ArticleTitleGenome remodeling in ciliated protozoa Annual Review of Microbiology 56 489–520 Occurrence Handle10.1146/annurev.micro.56.012302.160916
DM Prescott (1999) ArticleTitleThe evolutionary scrambling and developmental unscabling of germlike genes in hypotrichous ciliates Nucleic Acids Research 27 1243–1250 Occurrence Handle10.1093/nar/27.5.1243
DM Prescott (2000) ArticleTitleGenome gymnastics: unique modes of DNA evolution and processing in ciliates Nature Reviews Genetics 1 IssueID3 191–198 Occurrence Handle10.1038/35042057
DM Prescott A Ehrenfeucht G Rozenberg (2001) ArticleTitleMolecular operations for DNA processing in hypotrichous ciliates European Journal of Protistology 37 241–260 Occurrence Handle10.1078/0932-4739-00807
DB West (1996) Introduction to Graph Theory Prentice Hall Upper Saddle River, NJ
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Harju, T., Li, C., Petre, I. et al. Parallelism in Gene Assembly. Nat Comput 5, 203–223 (2006). https://doi.org/10.1007/s11047-005-4462-0
Issue Date:
DOI: https://doi.org/10.1007/s11047-005-4462-0