105 Pseudoknots PPTs View free & download

Classifying Pseudoknots PowerPoint PPT Presentation

Classifying Pseudoknots - Makes RNA secondary structure prediction NP-complete. Looks pretty simple... D) Mouse mammary tumor virus E) pea enation mosaic virus F) Simian retrovirus ...

Makes RNA secondary structure prediction NP-complete. Looks pretty simple... D) Mouse mammary tumor virus E) pea enation mosaic virus F) Simian retrovirus ...

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Structural Alignment of Pseudoknotted RNAs PowerPoint PPT Presentation

Structural Alignment of Pseudoknotted RNAs - Modern RNA world hypothesis: There are many undetected functional ncRNAs. [ Eddy Nature Reviews (2001) ... members of an RNA family as query and target. Align ...

Modern RNA world hypothesis: There are many undetected functional ncRNAs. [ Eddy Nature Reviews (2001) ... members of an RNA family as query and target. Align ...

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Topological Methods for RNA Pseudoknots PowerPoint PPT Presentation

Topological Methods for RNA Pseudoknots - Topological Representation and Classification. Thermodynamic Calculations ... IMA Annual Program Year Workshop: RNA in Biology, Bioengineering and Nanotechnology. ...

Topological Representation and Classification. Thermodynamic Calculations ... IMA Annual Program Year Workshop: RNA in Biology, Bioengineering and Nanotechnology. ...

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An efficient multiple alignment method for RNA secondary structures including pseudoknots PowerPoint PPT Presentation

An efficient multiple alignment method for RNA secondary structures including pseudoknots - An efficient multiple alignment method for RNA secondary structures including pseudoknots ... Noyori Conference Hall, Nagoya University, Japan ...

An efficient multiple alignment method for RNA secondary structures including pseudoknots ... Noyori Conference Hall, Nagoya University, Japan ...

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Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots PowerPoint PPT Presentation

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots - wd. wm. wam/2 per mismatched base. wb. wr. wa= (wb wr)/2 ... wd wd 0 wm. A C G U G U G A U G G G A G G U A C A A. U G C U A U A A U A G A U. cost to align ' ...

wd. wm. wam/2 per mismatched base. wb. wr. wa= (wb wr)/2 ... wd wd 0 wm. A C G U G U G A U G G G A G G U A C A A. U G C U A U A A U A G A U. cost to align ' ...

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RNA structure: tRNA PowerPoint PPT Presentation

RNA structure: tRNA - Chercher un algorithme exact f t (mais sans garantie de temps) ... Chercher une heuristique d'approximation. Contraindre les donn es du probl me ...

Chercher un algorithme exact f t (mais sans garantie de temps) ... Chercher une heuristique d'approximation. Contraindre les donn es du probl me ...

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RNA Secondary Structure Prediction PowerPoint PPT Presentation

RNA Secondary Structure Prediction - RNA Secondary Structure Prediction Dynamic Programming Approaches Sarah Aerni http://www.tbi.univie.ac.at/

RNA Secondary Structure Prediction Dynamic Programming Approaches Sarah Aerni http://www.tbi.univie.ac.at/

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DNA2: Last week's take home lessons PowerPoint PPT Presentation

DNA2: Last week's take home lessons - DNA2: Last week's take home lessons Comparing types of alignments & algorithms Dynamic programming (DP) Multi-sequence alignment Space-time-accuracy tradeoffs

DNA2: Last week's take home lessons Comparing types of alignments & algorithms Dynamic programming (DP) Multi-sequence alignment Space-time-accuracy tradeoffs

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On The RNA Structure Prediction Problems: Structural Inference Technique and Other Recent Algorithms PowerPoint PPT Presentation

On The RNA Structure Prediction Problems: Structural Inference Technique and Other Recent Algorithms - free energy. Best result without Pseudoknot: O(n ) time [1] ... We further improve it to O(nm2 log n) time and O(m2 log n) space. ...

free energy. Best result without Pseudoknot: O(n ) time [1] ... We further improve it to O(nm2 log n) time and O(m2 log n) space. ...

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A Bioinformatics Approach to Improving the Prediction of Programmed Ribosomal Frameshifting PowerPoint PPT Presentation

A Bioinformatics Approach to Improving the Prediction of Programmed Ribosomal Frameshifting - ... tested sequences in our experiments were taken from the PseudoBase and RECODE. ... RECODE contains the translational recoding events of PRFs in various ...

... tested sequences in our experiments were taken from the PseudoBase and RECODE. ... RECODE contains the translational recoding events of PRFs in various ...

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RNA Folding Algorithms PowerPoint PPT Presentation

RNA Folding Algorithms - (i,j) is the max number of basepairs in subsequence i..j (i,j) ... p-orbital conjugation. Induced polarity. Van der Waals forces. Loop closure. Tetraloops, etc. ...

(i,j) is the max number of basepairs in subsequence i..j (i,j) ... p-orbital conjugation. Induced polarity. Van der Waals forces. Loop closure. Tetraloops, etc. ...

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CS273A - ... X chromosome inactivation in mammals Xist X inactive-specific transcript Microarrays, Next Gen(eration) Sequencing etc. End Results Slide 38 Slide ...

... X chromosome inactivation in mammals Xist X inactive-specific transcript Microarrays, Next Gen(eration) Sequencing etc. End Results Slide 38 Slide ...

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The Search for Small Regulatory RNA PowerPoint PPT Presentation

The Search for Small Regulatory RNA - Role of RNA-binding protein Hfq How to identify sRNA? Label RNA with 32P; Isolate, characterize Microarray detection Shotgun clone by size class, sequence Functional ...

Role of RNA-binding protein Hfq How to identify sRNA? Label RNA with 32P; Isolate, characterize Microarray detection Shotgun clone by size class, sequence Functional ...

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BCB 444/544 - BCB 444/544 Lecture 25 More RNA Structure BCB 544 Projects #25_Oct19

BCB 444/544 Lecture 25 More RNA Structure BCB 544 Projects #25_Oct19

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RNA: Secondary Structure Prediction and Analysis PowerPoint PPT Presentation

RNA: Secondary Structure Prediction and Analysis - Silence an mRNA by base pairing with some sequence on the mRNA. miRNA Pathway Illustration siRNA ... Steps Find a perfect match ... David Mount Energy ...

Silence an mRNA by base pairing with some sequence on the mRNA. miRNA Pathway Illustration siRNA ... Steps Find a perfect match ... David Mount Energy ...

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RNA base pairing self consistent mean field approach PowerPoint PPT Presentation

RNA base pairing self consistent mean field approach - How to recognize a brave protein calculator ? rescue drowning babies ? take a job with a Liechtenstein Treuhander ? administrator in the Kenyan electoral commission ? ...

How to recognize a brave protein calculator ? rescue drowning babies ? take a job with a Liechtenstein Treuhander ? administrator in the Kenyan electoral commission ? ...

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Gene Ontology (GO) PowerPoint PPT Presentation

Gene Ontology (GO) - C E N T R F O R I N T E G R A T I V E E B I O I N F O R M A T I C S V U Master Course DNA/Protein Structure-function Analysis and Prediction Lecture 12 DNA/RNA ...

C E N T R F O R I N T E G R A T I V E E B I O I N F O R M A T I C S V U Master Course DNA/Protein Structure-function Analysis and Prediction Lecture 12 DNA/RNA ...

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CSE182-L18 - CSE182-L18 Population Genetics

CSE182-L18 Population Genetics

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Telomerase RNA PowerPoint PPT Presentation

Telomerase RNA - Telomerase RNA (TER): Sequential and Structural Characteristics ... Tools and Specific Problems of Yeast TER ... The Problems in the case of yeast TER: ...

Telomerase RNA (TER): Sequential and Structural Characteristics ... Tools and Specific Problems of Yeast TER ... The Problems in the case of yeast TER: ...

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Genome Wide Searches for RNA Secondary Structure Motifs PowerPoint PPT Presentation

Genome Wide Searches for RNA Secondary Structure Motifs - Genome Wide Searches for RNA Secondary Structure Motifs Russell S. Hamilton Davis Lab Wellcome Trust Centre for Cell Biology Drosophila melanogaster

Genome Wide Searches for RNA Secondary Structure Motifs Russell S. Hamilton Davis Lab Wellcome Trust Centre for Cell Biology Drosophila melanogaster

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Folie 1 - Aptamers have been selected which bind nucleic acid, proteins, small organic compounds. These novel molecules have many potential uses in medicine and technology ...

Aptamers have been selected which bind nucleic acid, proteins, small organic compounds. These novel molecules have many potential uses in medicine and technology ...

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Prediction of RNA structure PowerPoint PPT Presentation

Prediction of RNA structure - The DNA contains the code to all of the essential machinery of the cell, ... It is conjectured, and empirically shown that RNA has the polymer-zeta property ...

The DNA contains the code to all of the essential machinery of the cell, ... It is conjectured, and empirically shown that RNA has the polymer-zeta property ...

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????????F????? ?? ???a PowerPoint PPT Presentation

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Presentaci - Title: Presentaci n de PowerPoint Author: MJTORRES Last modified by: pc Created Date: 11/10/2004 2:53:03 PM Document presentation format: Presentaci n en pantalla (4:3)

Title: Presentaci n de PowerPoint Author: MJTORRES Last modified by: pc Created Date: 11/10/2004 2:53:03 PM Document presentation format: Presentaci n en pantalla (4:3)

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The RNA Ontology RNAO PowerPoint PPT Presentation

The RNA Ontology RNAO - Commitment to common upper ontology (BFO) ... alignment and phylogeny (Rob Knight) Rfam (Alex Bateman) 2D to 3D structure (Alain Laederach) ...

Commitment to common upper ontology (BFO) ... alignment and phylogeny (Rob Knight) Rfam (Alex Bateman) 2D to 3D structure (Alain Laederach) ...

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RNA Secondary Structure Prediction - Introduction to RNA Sequence/Structure Analysis. RNAs have many structural and ... Mutagenic analysis of the SARS-CoV shift site and mass spectrometry of an ...

Introduction to RNA Sequence/Structure Analysis. RNAs have many structural and ... Mutagenic analysis of the SARS-CoV shift site and mass spectrometry of an ...

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Stochastic Context Free Grammars PowerPoint PPT Presentation

Stochastic Context Free Grammars - (equivalent to finite automata & HMM's) (equivalent to SCFG's & pushdown automata) ... A in a cell cellA to the two cells cellB and cellC corresponding to B and C in ...

(equivalent to finite automata & HMM's) (equivalent to SCFG's & pushdown automata) ... A in a cell cellA to the two cells cellB and cellC corresponding to B and C in ...

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17.1 Roles of RNA Molecules PowerPoint PPT Presentation

17.1 Roles of RNA Molecules - Hydrophobicity. 17.2 Interactions of RNA Molecules. 3. Hydrophobicity. Self-complementary regions undergo complementary base pairing ...

Hydrophobicity. 17.2 Interactions of RNA Molecules. 3. Hydrophobicity. Self-complementary regions undergo complementary base pairing ...

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REPLICACIN VIRAL: ESTRATEGIAS DE RNA y DNA VIRUS PowerPoint PPT Presentation

REPLICACIN VIRAL: ESTRATEGIAS DE RNA y DNA VIRUS - estructuras secundarias: tallos o stems, horquillas o hairpin loops ... Distintas estructuras de IRES. A. Poliovirus; B. Virus de la encefalomiocarditis; C. HCV ...

estructuras secundarias: tallos o stems, horquillas o hairpin loops ... Distintas estructuras de IRES. A. Poliovirus; B. Virus de la encefalomiocarditis; C. HCV ...

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Improving Free Energy Functions for RNA Folding PowerPoint PPT Presentation

Improving Free Energy Functions for RNA Folding - May be possible to destroy specific sequences of RNA (to ... Crossover. P1. P2. C1. C2. Fit stems of P2 into C1 or C2 randomly. Placement must be conflict free. ...

May be possible to destroy specific sequences of RNA (to ... Crossover. P1. P2. C1. C2. Fit stems of P2 into C1 or C2 randomly. Placement must be conflict free. ...

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A Framework for Modeling DNA Based Nanorobotical Devices PowerPoint PPT Presentation

A Framework for Modeling DNA Based Nanorobotical Devices - Title: DNAModeller: Modelling DNA Based Nanodevices Author: Sudheer Last modified by: Sudheer Created Date: 5/31/2006 4:52:14 PM Document presentation format

Title: DNAModeller: Modelling DNA Based Nanodevices Author: Sudheer Last modified by: Sudheer Created Date: 5/31/2006 4:52:14 PM Document presentation format

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Folding RNA a confluence of biology, mathematics, and physics PowerPoint PPT Presentation

Folding RNA a confluence of biology, mathematics, and physics - Folding RNA a confluence of biology, mathematics, and physics A. Zee Institute for Theoretical Physics University of California Santa Barbara, CA, USA

Folding RNA a confluence of biology, mathematics, and physics A. Zee Institute for Theoretical Physics University of California Santa Barbara, CA, USA

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Coding for DNA Computing: Combinatorial and Biophysical Aspects PowerPoint PPT Presentation

Coding for DNA Computing: Combinatorial and Biophysical Aspects - (Presence of Long Subsequence and its Reverse Complement Lead to Stabilization ) ... Hamming, Reverse Complement Hamming Distance at Least d. Longest Length ...

(Presence of Long Subsequence and its Reverse Complement Lead to Stabilization ) ... Hamming, Reverse Complement Hamming Distance at Least d. Longest Length ...

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Genomics - Lecture 19A: Protein-protein interactions Complexity: Multibody interaction Diversity: Various interaction types Specificity: ...

Lecture 19A: Protein-protein interactions Complexity: Multibody interaction Diversity: Various interaction types Specificity: ...

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Molecular Tools for Studying Genes and Gene Activity PowerPoint PPT Presentation

Molecular Tools for Studying Genes and Gene Activity - Chapter 5 Molecular Tools for Studying Genes and Gene Activity Electrophoresis of Large DNA Special techniques are required for DNA fragments larger than about 1 ...

Chapter 5 Molecular Tools for Studying Genes and Gene Activity Electrophoresis of Large DNA Special techniques are required for DNA fragments larger than about 1 ...

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Bioinformatics: Applications PowerPoint PPT Presentation

Bioinformatics: Applications - Aside of being DNA's 'messenger', RNA performs functions itself ... 5' dangling -0.9 stacking -1.8 stacking -2.1 stacking. G= -4.6 KCAL/MOL 5.9 4nt loop ...

Aside of being DNA's 'messenger', RNA performs functions itself ... 5' dangling -0.9 stacking -1.8 stacking -2.1 stacking. G= -4.6 KCAL/MOL 5.9 4nt loop ...

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Ontological relations and computable definitions for sequences at DNA, RNA and protein levels PowerPoint PPT Presentation

Ontological relations and computable definitions for sequences at DNA, RNA and protein levels - Karen Eilbeck 7/22/08 ... Karen Eilbeck 7/22/08. Ontological Relations for Sequences at DNA, RNA, and protein levels ... Karen Eilbeck 7/22/08. What is a ...

Karen Eilbeck 7/22/08 ... Karen Eilbeck 7/22/08. Ontological Relations for Sequences at DNA, RNA, and protein levels ... Karen Eilbeck 7/22/08. What is a ...

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Welcome to My Molecular Biology Lecture PowerPoint PPT Presentation

Welcome to My Molecular Biology Lecture - Dedicated to the structure of DNA and the processes that propagate (??) ... are displaced by base-base interactions, which creates disorder/hydrophobicity ...

Dedicated to the structure of DNA and the processes that propagate (??) ... are displaced by base-base interactions, which creates disorder/hydrophobicity ...

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Application of Algorithm Research to Molecular Biology PowerPoint PPT Presentation

Application of Algorithm Research to Molecular Biology - Cut the DNA in each YAC clone and clone into overlapping cosmid clones. 104 bp. Duplicate the cosmid and then cut the copies randomly. ...

Cut the DNA in each YAC clone and clone into overlapping cosmid clones. 104 bp. Duplicate the cosmid and then cut the copies randomly. ...

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RNA secondary structure PowerPoint PPT Presentation

RNA secondary structure - Case 4: Bifurcation. combining two optimal substructures i, k and k 1, j. k ... pushdown stack is used to deal with bifurcated structures. Traceback Pseudocode ...

Case 4: Bifurcation. combining two optimal substructures i, k and k 1, j. k ... pushdown stack is used to deal with bifurcated structures. Traceback Pseudocode ...

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Viral Encephalitis PowerPoint PPT Presentation

Viral Encephalitis - Viral Encephalitis Dan Karlin, Jenny Richmond, Chiemi Suzuki BIO 4158: Microbiology and Bioterrorism Dr. Zubay April 20, 2004 Roadmap Introduction History and ...

Viral Encephalitis Dan Karlin, Jenny Richmond, Chiemi Suzuki BIO 4158: Microbiology and Bioterrorism Dr. Zubay April 20, 2004 Roadmap Introduction History and ...

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Initial Proposal for the RNA Alignment Ontology PowerPoint PPT Presentation

Initial Proposal for the RNA Alignment Ontology - Explicitly annotate correspondences at the level where they occur ... Ryan Kennedy. Julia Goodrich. Meg Pirrung. Reece Gesumaria. Trp project: Irene Majerfeld ...

Explicitly annotate correspondences at the level where they occur ... Ryan Kennedy. Julia Goodrich. Meg Pirrung. Reece Gesumaria. Trp project: Irene Majerfeld ...

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RNA Secondary Structure Prediction - Insertions & Deletions. Images Eddy et al. Covariance Model ... Not suitable for searches of large RNA. Structural complexity of large RNA cannot be modeled ...

Insertions & Deletions. Images Eddy et al. Covariance Model ... Not suitable for searches of large RNA. Structural complexity of large RNA cannot be modeled ...

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CS273A - ... (long intergenic non coding RNAs) X chromosome inactivation in mammals Xist X inactive-specific transcript Microarrays, Next Gen(eration) ...

... (long intergenic non coding RNAs) X chromosome inactivation in mammals Xist X inactive-specific transcript Microarrays, Next Gen(eration) ...

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Towards the sequence design preventing pseudoknot formation PowerPoint PPT Presentation

Towards the sequence design preventing pseudoknot formation - Information is encoded into DNA strings over adenine (A), cytosine (C), guanine ... Resulting DNA strings are decoded using such techniques as Gel-electrophoresis ...

Information is encoded into DNA strings over adenine (A), cytosine (C), guanine ... Resulting DNA strings are decoded using such techniques as Gel-electrophoresis ...

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RNA secondary structure prediction - Pseudo-knots: Cause problems to ordinary RNA folding. algorithms. ... with the maximal number of base pairs under the pseudo-knot exclusion constraint. ...

Pseudo-knots: Cause problems to ordinary RNA folding. algorithms. ... with the maximal number of base pairs under the pseudo-knot exclusion constraint. ...

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RNA secondary structure - ... structure. RNA is (usually) single-stranded. The nucleotides want' to pair with their Watson-Crick complements (AU, GC) They may settle' for a wobble pair (GU) ...

... structure. RNA is (usually) single-stranded. The nucleotides want' to pair with their Watson-Crick complements (AU, GC) They may settle' for a wobble pair (GU) ...

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Prediction of RNA PowerPoint PPT Presentation

Prediction of RNA - Dot matrix analysis, Global Energy Minimization Methods, Mfold, VIENNA RNA package ... Jaeger et al., 1989, 1990, Zuker, 1994 MFOLD ...

Dot matrix analysis, Global Energy Minimization Methods, Mfold, VIENNA RNA package ... Jaeger et al., 1989, 1990, Zuker, 1994 MFOLD ...

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Some OffLattice models incorporate energy functions. Such as hydrogen bonding, electrostatic forces, PowerPoint PPT Presentation

Some OffLattice models incorporate energy functions. Such as hydrogen bonding, electrostatic forces, - Some Off-Lattice models incorporate energy functions. Such as ... The energy from these forces is computed and added together ... Structural Classification of Proteins (SCOP) ...

Some Off-Lattice models incorporate energy functions. Such as ... The energy from these forces is computed and added together ... Structural Classification of Proteins (SCOP) ...

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103105 RNA Structure PowerPoint PPT Presentation

103105 RNA Structure - 12:10 PM IG Faculty Seminar in 101 Ind Ed II. Plant Steroid ... Bassham,Thomas Baum, Jeff Essner, Kristen Johansen, Jo Anne Powell-Coffman, Roger Wise, etc. ...

12:10 PM IG Faculty Seminar in 101 Ind Ed II. Plant Steroid ... Bassham,Thomas Baum, Jeff Essner, Kristen Johansen, Jo Anne Powell-Coffman, Roger Wise, etc. ...

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Prediction of RNA - Includes stacking, bulge, internal, and hairpin loop terms. Start from center because the center line is location of hairpin loops ...

Includes stacking, bulge, internal, and hairpin loop terms. Start from center because the center line is location of hairpin loops ...

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Introduction to RNA Bioinformatics PowerPoint PPT Presentation

Introduction to RNA Bioinformatics - Nat Rev Mol Cell Biol. 2005 May;6(5):376-85 microRNA Mattick, J.S. (2004) The hidden genetic program of complex organisms. Scientific American 291 (4): 60-67.

Nat Rev Mol Cell Biol. 2005 May;6(5):376-85 microRNA Mattick, J.S. (2004) The hidden genetic program of complex organisms. Scientific American 291 (4): 60-67.

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BCB 444/544 - Chp 8 - pp 97 - 112. Wed Oct 24 - Lecture 27 (will not be ... 1.6 kcal/mole. Why 1.2 vs 1.6? Basepair. What gives here? C Staben 2005. Energy minimization: ...

Chp 8 - pp 97 - 112. Wed Oct 24 - Lecture 27 (will not be ... 1.6 kcal/mole. Why 1.2 vs 1.6? Basepair. What gives here? C Staben 2005. Energy minimization: ...

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Welcome to My Molecular Biology Lecture - Dedicated to the structure of DNA and the processes that propagate (??) ... 3. Two different models illustrate structure a DNA double helix. Schematic model ...

Dedicated to the structure of DNA and the processes that propagate (??) ... 3. Two different models illustrate structure a DNA double helix. Schematic model ...

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Introduction to bioinformatics Lecture 2 Genes and Genomes PowerPoint PPT Presentation

Introduction to bioinformatics Lecture 2 Genes and Genomes - Transcription Translation = Expression. But DNA can also be transcribed into non-coding RNA ... very early on ('Celtic gene') Autosomal, recessive, ...

Transcription Translation = Expression. But DNA can also be transcribed into non-coding RNA ... very early on ('Celtic gene') Autosomal, recessive, ...

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Identification of noncoding RNA with the ERPIN program PowerPoint PPT Presentation

Identification of noncoding RNA with the ERPIN program - Subjective and painful descriptor generation ... SECIS (Selenocysteine Insertion Sequence) ncRNA detection ... Selenocysteine Insertion Sequence. required for ...

Subjective and painful descriptor generation ... SECIS (Selenocysteine Insertion Sequence) ncRNA detection ... Selenocysteine Insertion Sequence. required for ...

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Pseudoknots PowerPoint PPT Presentations