Secondary Structure Analysis of Xenopus 5S rRNA

1997/8/19


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目錄

Secondary Structure Analysis of Xenopus 5S rRNA

Significance of Studying RNA Structure

Characteristic Features of A?RNA Secondary Structure

True Knots

Pseudoknot

Methods to Study RNA Secondary Structure

RNA Folding Pathways

Energy Rules and Principle?of Structure Prediction

Stacking Energies

Stacking Is Not All Symmetric

Loop Destabilization Energy (I): Interior and Bulge Loops

Loop Destabilization Energy (II): Hairpin Loops

The Free Energy of A Given RNA Secondary Structure

Format of A "Connect" File

Discussion 2-1

Prediction of Suboptimal Structures

What Is Energy Increment?

Rationale

Energy Dotplot

P-Num Plot

Discussion

Difficulties in Detecting Funtional RNA Elements

Assumption of the Methods to Determine Functional Elements

Operational Definition of IFMs

Selection Advantage of IFMs

Functional RNA elements are IFMs

Prediction Accuracy of Functional RNA Elements

Limitation

How to set up constraints?

Demo 4-4

RNase cut Conformation

Initiation File for Single-stranded Constraint

Job Submission Using Initiation File

Exercise 4-3

Initiation File for Double-stranded Constraint

Structure Refinement is a Recursive Procedure

Formation of Compensatory Mutations (Covariation)

Demo 4-5

Use “xen5s.dna” to Search “genembl” Databank

Exercise 4-4

Use FastA Output As a List File

Get a Pretty Alignment Output

Covariations Found

Single-Stranded Regions Are Conserved in 5S rRNA

作者:楊永正實驗室

電子郵件: ang@ym.edu.tw

首頁: http://140.110.34.65/binfo-i/slides.htm

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