Workshop W6 Tutorial on RNA secondary structure

Nov 02, 2014

10 likes | 117 Views

Workshop W6 Tutorial on RNA secondary structure. Alain Laederach Slides available at: http://ribosnitch.bio.unc.edu/Downloads/RNA2013 / #RNA2013, @ alaederach.

Share Presentation

Embed Code

Link

rna2013
downloads rna2013
alain laederach
rna secondary structure
workshop w6 tutorial

nita-barron

Download Presentation

Workshop W6 Tutorial on RNA secondary structure

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

Workshop W6Tutorial on RNA secondary structure Alain Laederach Slides available at: http://ribosnitch.bio.unc.edu/Downloads/RNA2013/ #RNA2013, @alaederach

RNA Secondary Structure

RNA Secondary Structure. RNA Structure Prediction. FoldRNA Various graphic display options MFold PlotFold StemLoop. Structural Prediction Limitations. Gunnar von Heijne 1987

936 views • 59 slides

RNA secondary structure prediction and runtime optimization

RNA secondary structure prediction and runtime optimization. Greg Goldgof October 5, 2006 CS374 Presentation Stanford University. Presentation Overview. CONTRAfold: probabilistic RNA folding. Background on RNA secondary structure prediction.

745 views • 45 slides

RNA Secondary Structure Prediction

RNA Secondary Structure Prediction. Lecture 11: June 13, 2006 Algorithms of Molecular Biology. Introduction to RNA Sequence/Structure Analysis. RNAs have many structural and functional uses Translation Transcription RNA splicing RNA processing and editing cellular localization catalysis.

1.25k views • 84 slides

RNA Secondary Structure Prediction

RNA Secondary Structure Prediction. Dynamic Programming Approaches Sarah Aerni. http://www.tbi.univie.ac.at/. RNA folding Dynamic programming for RNA secondary structure prediction Covariance model for RNA structure prediction. Outline. RNA Basics. 3 Hydrogen Bonds – more stable.

1.46k views • 22 slides

RNA Secondary Structure Prediction

RNA Secondary Structure Prediction. RNA is a single-stranded chain of the nucleotides A, C, G, and U. The string of nucleotides specifies the linear structure of the RNA strand. When RNA folds, complementary nucleotides form base pairs (CG and AU).

933 views • 36 slides

RNA Secondary Structure Prediction

RNA Secondary Structure Prediction. 16s rRNA. RNA Secondary Structure. Pseudoknot. Dangling end. Single- Stranded. Interior Loop. Bulge. Junction (Multiloop). Stem. Hairpin loop. Image– Wuchty. RNA secondary structure. G A A A G G A-U U-G C-G

344 views • 16 slides

RNA Secondary Structure

RNA Secondary Structure. aagacuucggaucuggcgacaccc uacacuucggaugacaccaaagug aggucuucggcacgggcaccauuc ccaacuucggauuuugcuaccaua aagccuucggagcgggcguaacuc. Hairpin Loops. Interior loops. Stems. Multi-branched loop. Bulge loop. A Context Free Grammar. S  AB Nonterminals: S, A, B

520 views • 33 slides

6.5 RNA Secondary Structure

6.5 RNA Secondary Structure. RNA Secondary Structure. RNA. String B = b 1 b 2  b n over alphabet { A, C, G, U }. Secondary structure. RNA is single-stranded so it tends to loop back and form base pairs with itself. This structure is essential for understanding behavior of molecule. C.

533 views • 8 slides

RNA Secondary Structure

RNA Secondary Structure. aagacuucggaucuggcgacaccc uacacuucggaugacaccaaagug aggucuucggcacgggcaccauuc ccaacuucggauuuugcuaccaua aagccuucggagcgggcguaacuc. Stochastic Context Free Grammars. In an analogy to HMMs, we can assign probabilities to transitions: Given grammar

455 views • 30 slides

RNA Secondary Structure

RNA Secondary Structure. aagacuucggaucuggcgacaccc uacacuucggaugacaccaaagug aggucuucggcacgggcaccauuc ccaacuucggauuuugcuaccaua aagccuucggagcgggcguaacuc. RNA and Translation. RNA and Splicing. Hairpin Loops. Interior loops. Stems. Multi-branched loop. Bulge loop.

535 views • 37 slides

RNA secondary structure

6.096 – Algorithms for Computational Biology. RNA secondary structure. Lecture 1 - Introduction Lecture 2 - Hashing and BLAST Lecture 3 - Combinatorial Motif Finding Lecture 4 - Statistical Motif Finding Lecture 5 - Sequence alignment and Dynamic Programming. 8. 2. 6. 9. 5. 7. 1.

1.63k views • 108 slides

Prediction of Secondary Structure of RNA

Prediction of Secondary Structure of RNA. Swetha Nandyala. Overview. Introduction How RNA Secondary Structure is obtained ? Various types of loops possible in RNA Secondary Structure Motivation Resource Implements the Algorithms to be Understood Algorithm Nussinovs RNA Folding Example.

501 views • 18 slides

RNA secondary structure prediction

Doug Raiford Lesson 7. RNA secondary structure prediction. Why do we care. RNA World Hypothesis RNA world evolved into the DNA and protein world DNA advantage: greater chemical stability Protein advantage: more flexible and efficient enzymes ( biomolecules that catalyze)

654 views • 28 slides

RNA Secondary Structure Prediction

RNA Secondary Structure Prediction. Spring 2010. Objectives. Can we predict the structure of an RNA? Can we predict the structure of a protein?. RNA: Hypothesis and exclusions. Single stranded chain A RNA molecule is a string of n characters R=r 1 r 2 …r n such that r i  {A,C,G,U}

513 views • 32 slides

RNA: Secondary Structure Prediction and Analysis

RNA: Secondary Structure Prediction and Analysis. Outline. RNA Folding Dynamic Programming for RNA Secondary Structure Prediction Covariance Model for RNA Structure Prediction Small RNAs: Identification and Analysis. Section 1: RNA Folding. RNA bases: A,C,G,U Canonical Base Pairs A-U

1.61k views • 94 slides

RNA Bioinformatics Genes and Secondary Structure

RNA Bioinformatics Genes and Secondary Structure. Anne Haake Rhys Price Jones & Tex Thompson. Types of RNA. Coding mRNA (messenger) Non-Coding rRNA (ribosomal) tRNA (transfer) snRNA (small nuclear;splicing) RNAseP (ribozyme) siRNA (small inhibitory) Others…. RNA genes?. Recall:

426 views • 28 slides

RNA Secondary Structure

RNA Secondary Structure. aagacuucggaucuggcgacaccc uacacuucggaugacaccaaagug aggucuucggcacgggcaccauuc ccaacuucggauuuugcuaccaua aagccuucggagcgggcguaacuc. Decoding: the CYK algorithm. Given x = x 1 ....x N , and a SCFG G, Find the most likely parse of x

559 views • 44 slides

Arc-Segment Alignment for RNA Secondary Structure

Arc-Segment Alignment for RNA Secondary Structure. 指導教授：楊昌彪學生姓名：彭永興. The Longest Common Subsequence (LCS) Problem. A string : S 1 = “ TAGTCACG ” A subsequence of S 1 : deleting 0 or more symbols from S 1 (not necessarily consecutive). e.g. G , AGC , TATC , AGACG

220 views • 12 slides

Secondary Structure Prediction (Mostly RNA)

Secondary Structure Prediction (Mostly RNA). An example of RNA structure. RNA secondary structures. A real example - tRNA. Conserved structures. Building a grammar. An example grammar. Grammar for a protein motif. Example Hidden Markov Models.

230 views • 9 slides

RNA Secondary Structure

431 views • 27 slides

RNA Secondary Structure

RNA Secondary Structure. What is RNA? Definition of RNA secondary Structure RNA molecule evolution Algorithms for base pair maximisation Chomsky’s Linguistic Hierarchy Stochastic Context Free Grammars & Evolution Miscelaneous topics. Base Pairing From Przytycka. An Example: t-RNA.

470 views • 40 slides

RNA Secondary Structure Prediction

RNA Secondary Structure Prediction. Dynamic Programming Approaches Sarah Aerni. http://www.tbi.univie.ac.at/. RNA folding Dynamic programming for RNA secondary structure prediction. Outline. RNA Basics. RNA bases A,C,G,U Canonical Base Pairs A-U G-C

541 views • 16 slides

More Related