11. RNA Secondary Structure; Biological Functions and Predictions
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- čas přidán 19. 01. 2015
- MIT 7.91J Foundations of Computational and Systems Biology, Spring 2014
View the complete course: ocw.mit.edu/7-91JS14
Instructor: Christopher Burge
Lecture 11 is about RNA secondary structure. Prof. Christopher Burge begins with an introduction and biological examples of RNA structure. He then talks about two approaches for predicting structure: covariation and energy minimization.
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25:55 RNA part starts
26:56 RNA secondary structure
28:22 RNA secondary structure representation
31:12 A ribosome cracked open
35:10 What are the practical applications of knowing the ribosome structure?
36:10 ncRNAs: Challenges for Computational Biology
38:04 Covariation
40:52 The Mutual information statistic
52:34 Inferring secondary structure from covariation
54:03 Stundent asks: What would a covariation matrix for the given example look like?
56:18 What is needed for accurate inference of RNA secondary structure by covariation?
58:36 Student asks about more complex secondary structure configurations (archs crossing = pseudoknots)
1:01:10 Classes of ncRNAs
1:03:07 The Energy Minimization approach to inferring RNA secondary structure
1:04:24 How do Energy Minimization algorithms work?
1:09:46 Recursive maximization of base pairing
1:12:29 An example of bifurcation
1:15:20 Recursive Base Pair Maximization Algorithm
1:16:39 Home exercise
1:17:51 Base Pair Maximization Algorithm issues
1:18:28 Viral pseudoknosts and "kissing loops"
1:19:35 Methods using more sophisticated thermodynamic models
1:19:52 The Zuker algorithm
1:20:23 Links & References (mFold)
1:20:39 mFold Examples
25:50 RNA secondary structure
The slide titled "Architecture of TMHMM", Prof said that the minimum number of residues in the diagrammatic representation of the helix states is 4 might be only for illustration purposes, but as far as I understand, the number has to be 4 because the minimum of 4 residues is required to obtain a helix turn to form 1-> 4 H-bonding and hence the imposition of minimum length of helix residues to be 4
1:03 start for de novo folding algorithms
RNA Secondary Structure; Biological Functions and Predictions - MIT US
(On Sunday of April 2, 2023). On the Matter of RNA Secondary Structure (tRNAs, and Riboswitches [HIV Mechanism]) Biological Function and Predictions by MIT OpenCourseWare by PhD Christopher Burge: 1) Ribonucleic Acid and the Primordiality Therein just gives us an Glimpse of the Anabolism Nature logically allows via the concept of Inverse Entropy (Complementarity, Indirect Proportionality and Reactive Diametrics) but unlikely will allow, or should it, complete Annihilation or Entropy Acceleration leading to Inverse Singularity (i.e. Anti-matter Creation at CERN and Nazi Complex of Uranium-235 Radioactive Harnessing for Military Ends). If RNA was genuinely unstable, DNA would only be an Unstable form of a Lesser Reduction State within the Pentose Monosaccharide and Ensuing Polymerization. Rather, this is merely a continuation of Quanta Theory and the Relativity of Cosmological Significance. In Better times, will there be a completely de-programmable Matter and my hope herein ensues logically as to the Preservation of Olden and unknown Mysticism of Life itself but thereby its Sacrosanctity. I do not rejoice in the Disgusting Proliferation of Obtuse and Obnoxious Biohazardous Environment of this Typical Mindset of Synthetic Determinism and doubtedly anybody else either. At any rate, yeah I like to Further my depth and Ambidexterity in the Field of Biochemistry, but as it is broaden the Possibility and Pattern of this Toxic and rather Queer interpretation of Universal and Fundamental Principles also leads me Dire, Cataclysmic, and Foreboding Thoughts....PhD Christopher Burge, es geht gut zu lernen der Chemienatur und vermehren Weltgesundheit aber Umweltlernung auch Angelegenheit ist. Heil!
I still have a problem with understanding the mechanism of RNA Quadruplex folding. Can someone recommended me literature?
35:10 How someone could believe that this structure came about by chance as opposed to intelligent design is beyond me.
25:50 RNA secondary structure