Functional RNA sequences typically have structural elements that are highly conserved during evolution. Here we present an algorithmic method for multiple alignment of RNAs, taking into consideration both structural similarity and sequence identity. Furthermore, we performed a comparative analysis on pairing probability matrices of a set of aligned orthologous sequences and predicted the conserved secondary structure. Our alignment method outperforms the most widely used multiple alignment tool - Clustal W, and the structure prediction approach we proposed can generate a more accurate secondary structure for 5S rRNA compared to the existing approaches such as Alifold. In addition, our algorithms are efficient in terms of CPU time and memory usage compared to most existing methods for secondary structure prediction.
| Identifer | oai:union.ndltd.org:LACETR/oai:collectionscanada.gc.ca:QMM.82453 |
| Date | January 2005 |
| Creators | Yang, Qian, 1973- |
| Publisher | McGill University |
| Source Sets | Library and Archives Canada ETDs Repository / Centre d'archives des thèses électroniques de Bibliothèque et Archives Canada |
| Language | English |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Format | application/pdf |
| Coverage | Master of Science (School of Computer Science.) |
| Rights | All items in eScholarship@McGill are protected by copyright with all rights reserved unless otherwise indicated. |
| Relation | alephsysno: 002227264, proquestno: AAIMR12568, Theses scanned by UMI/ProQuest. |
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