Automated design of assemblable, modular, synthetic chromosomes

Sarah M. Richardson, Brian S. Olson, Jessica S. Dymond, Randal Burns, Srinivasan Chandrasegaran, Jef D. Boeke, Amarda Shehu, Joel S. Bader

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The goal of the Saccharomyces cerevisiae v2.0 project is the complete synthesis of a re-designed genome for baker's yeast. The resulting organism will permit systematic studies of eukaryotic chromosome structure that have been impossible to explore with traditional gene-at-a-time experiments. The efficiency of chemical synthesis of DNA does not yet permit direct synthesis of an entire chromosome, although it is now feasible to synthesize multi-kilobase pieces of DNA that can be combined into larger molecules. Designing a chromosome-sized sequence that can be assembled from smaller pieces has to date been accomplished by biological experts in a laborious and error-prone fashion. Here we pose DNA design as an optimization problem and obtain optimal solutions with a parallelizable dynamic programming algorithm.

Original languageEnglish (US)
Title of host publicationParallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers
Pages280-289
Number of pages10
EditionPART 2
DOIs
StatePublished - Aug 5 2010
Event8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009 - Wroclaw, Poland
Duration: Sep 13 2009Sep 16 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 2
Volume6068 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009
CountryPoland
CityWroclaw
Period9/13/099/16/09

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ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Richardson, S. M., Olson, B. S., Dymond, J. S., Burns, R., Chandrasegaran, S., Boeke, J. D., Shehu, A., & Bader, J. S. (2010). Automated design of assemblable, modular, synthetic chromosomes. In Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers (PART 2 ed., pp. 280-289). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6068 LNCS, No. PART 2). https://doi.org/10.1007/978-3-642-14403-5_30