TY - GEN
T1 - Optimizing restriction site placement for synthetic genomes
AU - Montes, Pablo
AU - Memelli, Heraldo
AU - Ward, Charles
AU - Kim, Joondong
AU - Mitchell, Joseph S.B.
AU - Skiena, Steven
PY - 2010
Y1 - 2010
N2 - Restriction enzymes are the workhorses of molecular biology. We introduce a new problem that arises in the course of our project to design virus variants to serve as potential vaccines: we wish to modify virus-length genomes to introduce large numbers of unique restriction enzyme recognition sites while preserving wild-type function by substitution of synonymous codons. We show that the resulting problem is NP-Complete, give an exponential-time algorithm, and propose effective heuristics, which we show give excellent results for five sample viral genomes. Our resulting modified genomes have several times more unique restriction sites and reduce the maximum gap between adjacent sites by three to nine-fold.
AB - Restriction enzymes are the workhorses of molecular biology. We introduce a new problem that arises in the course of our project to design virus variants to serve as potential vaccines: we wish to modify virus-length genomes to introduce large numbers of unique restriction enzyme recognition sites while preserving wild-type function by substitution of synonymous codons. We show that the resulting problem is NP-Complete, give an exponential-time algorithm, and propose effective heuristics, which we show give excellent results for five sample viral genomes. Our resulting modified genomes have several times more unique restriction sites and reduce the maximum gap between adjacent sites by three to nine-fold.
KW - Genome refactoring
KW - Restriction enyzme placement
KW - Synthetic biology
UR - https://www.scopus.com/pages/publications/79956291154
U2 - 10.1007/978-3-642-13509-5_29
DO - 10.1007/978-3-642-13509-5_29
M3 - Conference contribution
AN - SCOPUS:79956291154
SN - 3642135080
SN - 9783642135088
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 323
EP - 337
BT - Combinatorial Pattern Matching - 21st Annual Symposium, CPM 2010, Proceedings
T2 - 21st Annual Symposium on Combinatorial Pattern Matching, CPM 2010
Y2 - 21 June 2010 through 23 June 2010
ER -