Predicting RNA secondary structure using a stochastic conjunctive grammar
Date
2012-08-22
Authors
Zier-Vogel, Ryan
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
In this thesis I extend a class of grammars called conjunctive grammars to a
stochastic form called stochastic conjunctive grammars. This extension allows the
grammars to predict pseudoknotted RNA secondary structure. Since observing sec-
ondary structure is hard and expensive to do with today's technology, there is a need for computational solutions to this problem. A conjunctive grammar can handle
pseudoknotted structure because of the way one sequence is generated by combining
multiple parse trees.
I create several grammars that are designed to predict pseudoknotted RNA sec-
ondary structure. One grammar is designed to predict all types of pseudoknots and
the others are made to only predict a pseudoknot called H-type. These grammars are
trained and tested and the results are collected. I am able to obtain a sensitivity of over 75% and a speci city of over 89% on H-type pseudoknots
Description
Keywords
pseudoknot, RNA, grammar