Year of Publication


Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation




Computer Science

First Advisor

Dr. Jun Zhang


This thesis presents a new algorithm to predict the pre-microRNA secondary structure. An accurate prediction of the pre-microRNA secondary structure is important in miRNA informatics. Based on a recently proposed model, nucleotide cyclic motifs (NCM), to predict RNA secondary structure, we propose and implement a Modified NCM (MNCM) model with a physics-based scoring strategy to tackle the problem of pre-microRNA folding. Our microRNAfold is implemented using a global optimal algorithm based on the bottom-up local optimal solutions.

It has been shown that studying the functions of multiple genes and predicting the secondary structure of multiple related microRNA is more important and meaningful since many polygenic traits in animals and plants can be controlled by more than a single gene. We propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. The experimental results show that our algorithm is able to produce the optimal secondary structure of polycistronic microRNAs. The trend of speedups of our parallel algorithm matches that of theoretical speedups.

Conserved secondary structures are likely to be functional, and secondary structural characteristics that are shared between endogenous pre-miRNAs may contribute toward efficient biogenesis. So identifying conserved secondary structure is very meaningful and identifying conserved characteristics in RNA is a very important research field. After the characteristics are extracted from the secondary structures of RNAs, corresponding patterns or rules could be dug out and used.

We propose to use the conserved microRNA characteristics in two aspects: to improve prediction through knowledge base, and to classify the real specific microRNAs from pseudo microRNAs. Through statistical analysis of the performance of classification, we verify that the conserved characteristics extracted from microRNAs’ secondary structures are precise enough.

Gene suppression is a powerful tool for functional genomics and elimination of specific gene products. However, current gene suppression vectors can only be used to silence a single gene at a time. So we design an efficient poly-cistronic microRNA vector and the web-based tool allows users to design their own microRNA vectors online.