Formal Language Representation and Modeling of Bio-molecular Structures by Matrix Insertion-Deletion Systems

Wednesday, July 5, 2017 - 10:30 to Saturday, July 29, 2017 - 10:30
Room Aurigny
Talk abstract: 

David Searls initiated the representation of molecules as strings and modeled structures formed by the molecules using formal grammars. The work opened the doors to tackle many problems in computational biology like predicting pseudoknot structures of biomolecules. Subsequently, Sakakibara, Hausler, Eddy, Rivas, Umera and others introduced various grammar formalisms for modeling predominantly noticed bio-molecular structures such as stem-loop, pseduoknot, attenuator, clover-leaf, dumbbell. However, there is no unique grammar formalism that models all the structures discussed in literature. In this talk, we shall study a recently introduced grammar formalism namely matrix insertion-deletion systems. In this system, set of rules are applied in order which helps to synchronize the elements even at far. With this system, we will model several intra and inter molecular structures of DNA and RNA. We will also model parallel and anti-parallel beta sheets of protein molecules with the system.