TY - GEN
T1 - Designing RNA secondary structures in coding regions
AU - Yeasmin, Rukhsana
AU - Skiena, Steven
PY - 2012
Y1 - 2012
N2 - Sophisticated regulatory structures appear within highly-constrained coding regions of genes. We study the extent to which such structures can be constructed. Can such stem loops appear essentially anywhere within coding regions, or is the potential restricted to rare amino acid sequences? While predicting secondary structures of an RNA sequence is an extensively studied problem in computational biology, the inverse problem, designing sequences based on a known structure is also important. We work on a particular version of the inverse RNA folding problem, where our goal is to achieve a targeted energy level. For a particular RNA structure, we design sequences with the maximum and minimum folding energy while maintaining desired codon distribution. Our major contributions in work is to optimize RNA secondary structure under codon constraints via fast estimation of folding energies following local modification.
AB - Sophisticated regulatory structures appear within highly-constrained coding regions of genes. We study the extent to which such structures can be constructed. Can such stem loops appear essentially anywhere within coding regions, or is the potential restricted to rare amino acid sequences? While predicting secondary structures of an RNA sequence is an extensively studied problem in computational biology, the inverse problem, designing sequences based on a known structure is also important. We work on a particular version of the inverse RNA folding problem, where our goal is to achieve a targeted energy level. For a particular RNA structure, we design sequences with the maximum and minimum folding energy while maintaining desired codon distribution. Our major contributions in work is to optimize RNA secondary structure under codon constraints via fast estimation of folding energies following local modification.
KW - inverse RNA folding
KW - RNA structure prediction
KW - Synthetic biology
UR - https://www.scopus.com/pages/publications/84861127027
U2 - 10.1007/978-3-642-30191-9_28
DO - 10.1007/978-3-642-30191-9_28
M3 - Conference contribution
AN - SCOPUS:84861127027
SN - 9783642301902
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 299
EP - 314
BT - Bioinformatics Research and Applications - 8th International Symposium, ISBRA 2012, Proceedings
T2 - 8th International Symposium on Bioinformatics Research and Applications, ISBRA 2012
Y2 - 21 May 2012 through 23 May 2012
ER -