Document Type
Thesis
Date of Award
Spring 5-31-2013
Degree Name
Master of Science in Bioinformatics - (M.S.)
Department
Computer Science
First Advisor
Jason T. L. Wang
Second Advisor
Zhi Wei
Third Advisor
Mei Liu
Fourth Advisor
Usman W. Roshan
Abstract
Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To annotate an individual genome for a specific family of ncRNAs, a computational tool is interpreted to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a novel approach for such genome wide search of ncRNAs using the RNATOPS and Infernal software tools, which incorporates heuristic dynamic programming algorithms to carry out the sequence analysis using the profiles of RNA consensus secondary structures.
Genome wide search for ncRNAs from thirteen genomes is performed using RNATOPS and Infernal. The training set of ncRNA multiple sequence alignments is prepared from RFAM and homologous Genomes are retrieved from RNASTRAND database. Through the experiments, performance of each tool is analyzed and compared with respect to their ncRNA search accuracies. It is further interfered that Infernal, compared to RNATOPS, is more accurate in detecting an ncRNA in all the thirteen genomes tested.
Recommended Citation
Vasavada, Meghana S., "Genome wide search for pseudo knotted non-coding RNAs" (2013). Theses. 159.
https://digitalcommons.njit.edu/theses/159
