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 - 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

    Conference

    Conference8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009
    CountryPoland
    CityWroclaw
    Period9/13/099/16/09

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • Computer Science(all)

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