TY - GEN
T1 - Automated design of assemblable, modular, synthetic chromosomes
AU - Richardson, Sarah M.
AU - Olson, Brian S.
AU - Dymond, Jessica S.
AU - Burns, Randal
AU - Chandrasegaran, Srinivasan
AU - Boeke, Jef D.
AU - Shehu, Amarda
AU - Bader, Joel S.
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/77955104288
UR - https://www.scopus.com/pages/publications/77955104288#tab=citedBy
U2 - 10.1007/978-3-642-14403-5_30
DO - 10.1007/978-3-642-14403-5_30
M3 - Conference contribution
AN - SCOPUS:77955104288
SN - 3642144020
SN - 9783642144028
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 280
EP - 289
BT - Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers
T2 - 8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009
Y2 - 13 September 2009 through 16 September 2009
ER -