3 papers
q-bio.QM2018
RNAmountAlign: efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment
Amir H. Bayegan, Peter Clote
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should tak…
cs.DS2018
Minimum length RNA folding trajectories
Amir H. Bayegan, Peter Clote
The Kinfold and KFOLD programs for RNA folding kinetics implement the Gillespie algorithm to generate stochastic folding trajectories from an initial structure s to a target struct…
q-bio.BM2017
RNA folding kinetics using Monte Carlo and Gillespie algorithms?
Peter Clote, Amir H. Bayegan
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra p…