Course Overview
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Course Synopsis
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This course will help undergraduate students to understand the need, development, fundamentals and techniques in Bioinformatics. Several techniques such as pairwise sequence alignment and multiple sequence alignment, protein structure prediction as well as online tools will be discussed .Students will also able to understand basic central dogma of cell, different algorithms and biological data bases. Construction of bi-molecular networks will be discussed and analysis will be performed using Boolean state representations.
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Course Learning Outcomes
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At the end of this course students will have a better understandings of following terms:
- Introduction to Bioinformatics.
- Sequence Alignment techniques
- Molecular Evolution and Phylogeny Information
- Homology Modelling techniques
- Understandings of Biological data bases and algorithms
- Protein structure and sequence prediction techniques
- Introduction to Systems Biology
- Understanding of constructing bi-molecular networks and Boolean state representations.
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Course Calendar
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Week 01
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1
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Background of bioinformatics
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2
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Introduction to bioinformatics
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3
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Need for Bioinformatics - I
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4
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Need for Bioinformatics - II
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5
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Applications of Bioinformatics - I
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6
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Applications of Bioinformatics - II
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7
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Frontiers in Bioinformatics - I
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8
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Frontiers in Bioinformatics - II
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9
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Overview of Course Contents - I
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10
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Overview of Course Contents - II
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11
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Overview of Course Contents - III
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12
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Gene, mRNA and Protein Sequences
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Week 02
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17
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Storage of Biological Sequence Information
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21
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Similarities and Differences in Sequences
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22
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Pairwise Sequence Alignment-I
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23
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Pairwise Sequence Alignment-II
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24
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Pairwise Sequence Alignment-III
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27
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Identity vs. Similarity
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28
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Introduction to Alignment Approaches
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31
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Aligning Mutations in Sequences
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32
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Introduction to Dynamic Programming
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Week 03
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33
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Dynamic Programming - Essentials
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34
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Dynamic Programming Methodology
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35
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Needleman Wunsh Algorithm-I
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36
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Needleman Wunsh Algorithm-II
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37
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Needleman Wunsh Algorithm-III
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38
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Needleman Wunsh Algorithm-Example
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39
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Backtracking Alignments
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40
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Revisiting Global and Local Alignments
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42
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Example of Overlap Matches
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43
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Moving From global to local alignment
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44
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Smith Waterman Algorithm
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45
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Example of Smith Waterman Algorithm
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47
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Example of repeated alignment
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48
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Review of Traceback Strategies for Global, Overlap, Local and Repeated Alignments
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Week 04
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49
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Introduction to Scoring Alignments
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50
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Measuring alignments by scoring
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52
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Deriving scoring matrices
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55
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Introduction to Multiple Sequences Alignment
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56
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More on Multiple Sequence Alignment
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57
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Progressive Alignment for MSA
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60
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Introduction to BLAST - I
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61
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Introduction to BLAST - II
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Week 05
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65
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Introduction to FastA-I
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66
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Introduction to FastA-II
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70
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Biological Databases and Online Tools
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74
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Review of Sequence Alignment
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76
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Molecular evolution and phylogeny
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77
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Evolution of sequences
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78
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Concepts and Terminologies - I
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79
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Concepts and Terminologies - II
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80
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Algorithm and Techniques
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Week 06
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87
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DNA to RNA Sequences, Base Complementarity
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88
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Types of RNA and their Function
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89
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Significance of RNA Structures
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90
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RNA Folding, Energies of Folding
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91
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Calculating Energies of Folding - An Example
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92
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Types of RNA Secondary Structures - I
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93
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Types of RNA Secondary Structures - II
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94
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Types of RNA Secondary Structures - III
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95
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RNA Tertiary Structures
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96
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Circular Representation of RNA Structures
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Week 07
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97
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Experimental Methods for Determining RNA Strucutres
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98
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Strategies for RNA Structure Prediction
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99
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Dot Plots for RNA 2' Structure Prediction
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102
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Example - Zuker Algorithm
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103
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Zuker Algorithm - Flowchart
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105
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Dynamic Programming Approaches
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106
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Nussinov -Jacobson Algorithm Overview
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107
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NJ Algorithm Flowchart
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108
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Example - Jacobson Algorithm
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109
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Score Calculations and Traceback
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110
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Comparison of Algorithms
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111
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Web Resources: RNA Bricks
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Week 08
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113
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From DNA/RNA Sequences to Proteins
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114
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Coding of Amino Acids
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116
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ORF Extraction – A Flowchart
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118
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Application of MS in sequencing
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119
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Techniques for MS Proteomics
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120
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Types of MS-based proteomics
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122
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Two Approaches for Bottom Up Proteomics
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124
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Protein Identification
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125
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Protein Ionization Techniques
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126
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MS1 and Intact Protein Mass
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127
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Scoring Intact Protein Mass
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128
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Protein Fragmentation Techniques
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Week 09
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130
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Measuring Experimental Fragment's Mass
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131
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Calculating Theoretical Fragment's Mass
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132
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Peptide Sequence Tags
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133
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Extracting Peptide Sequence Tags
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134
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Using Peptide Sequence Tags in Protein Search
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135
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Scoring Peptide Sequence Tags
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136
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In silico Protein Fragmentation
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137
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In silico Fragment Comparison and Scoring
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138
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Protein Sequence Database Search Algorithm
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139
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Integrative Scoring Schemes
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140
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Large Scale Proteomics
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141
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Proteomics Data File Formats
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Week 10
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145
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Online Proteomics Tools - Mascot
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146
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Online Proteomics Tools - ProSight PTM
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147
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Example Case Study - I
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148
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Example Case Study - II
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149
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Example Case Study - III
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150
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Example Case Study - IV
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151
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Example Case Study - V
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152
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Example Case Study - VI
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153
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Properties of Amino Acids - I
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154
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Properties of Amino Acids - II
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155
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Properties of Amino Acids - III
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156
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Properties of Amino Acids - IV
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157
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Properties of Amino Acids - V
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158
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Structural Traits of Amino Acids - I
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159
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Structural Traits of Amino Acids - II
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160
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Structural Traits of Amino Acids - III
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Week 11
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161
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Structural Traits of Amino Acids - IV
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162
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Introduction to Protein Folding
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163
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Importance of Protein Folding
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164
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Computing Protein Folding Possibilities
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165
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Process of Protein Folding
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166
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Models of Protein Folding
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168
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Primary, Secondary, Tertiary and Quaternary Structures
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169
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Primary Structure of Proteins
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170
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Secondary Structures of Proteins - I
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171
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Secondary Structures of Proteins -II
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172
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Tertiary Structures of Proteins
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173
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Quaternary Structures of Proteins
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174
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Introduction to Protein Bond Angles
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Week 12
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176
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Structure Visualization - I
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177
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Structure Visualization - II
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178
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Experimental Determination of Protein Structure
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180
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Visualization Techniques
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181
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Online Resources for Protein Visualization
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182
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Types of Protein Visualizations
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183
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Introduction to Energy of Protein Structures
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184
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Calculating Energies of Protein Structures
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185
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Structure Determination for Energy Calculations
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186
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Review of Experimental Structure Determination
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187
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Protein Structures - Alpha Helices I
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188
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Protein Structures - Alpha Helices II
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189
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Protein Structures - Beta Sheets I
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190
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Protein Structures - Beta Sheets II
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Week 13
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191
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Protein Structures - Loops I
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192
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Protein Structures - Loops II
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193
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Protein Structures - Coils
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194
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Structure Classification - I
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195
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Structure Classification - II
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196
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Examples of Protein Domains
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198
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Classification Databases
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199
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Algorithms for Structure Classification
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200
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Protein Structure Comparison
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201
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Strategies for Structure Comparison - I
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202
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Strategies for Structure Comparison - II
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203
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Online Resources for Structure Comparison
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204
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Protein Structure Prediction
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205
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Predicting Secondary Structures
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Week 14
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206
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Introduction to Chou Fasman Algorithm
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207
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2’ Structures in Chou Fasman Algorithm
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208
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Chou Fasman Algorithm - I
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209
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Chou Fasman Algorithm - II
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210
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Chou Fasman Algorithm - III
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211
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Chou Fasman Algorithm - IV
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212
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Chou Fasman Algorithm – Flowchart I
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213
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Chou Fasman Algorithm – Flowchart II
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214
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Chou Fasman Algorithm – Flowchart III
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215
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Chou Fasman Algorithm – Improvements
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216
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Summary of Visualization, Classification and Prediction
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217
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Introduction to Homology modelling
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218
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Homology, Paralogy and Orthology
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Week 15
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219
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Workflow for Structural Modelling
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220
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Seven Steps to Homology Modelling - I
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221
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Seven Steps to Homology Modelling - II
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222
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Seven Steps to Homology Modelling - III
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223
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Seven Steps to Homology Modelling - IV
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224
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Seven Steps to Homology Modelling - V
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225
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Seven Steps to Homology Modelling - VI
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226
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Modeller for Homology Modelling
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227
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Fold Recognition Threading I
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228
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Fold Recognition Threading II
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229
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Fold Recognition Threading III
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230
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Online Tools for Threading - iTasser
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231
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Advantages and Disadvantages of Threading
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232
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3D-1D Bowie Algorithm
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233
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Introduction to Ab-Initio Modelling
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234
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Rationale of Ab Initio Modelling
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235
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Strategies for Ab Initio Modelling
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236
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Energy States of Folded Proteins
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237
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Local versus Global Minima
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238
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Pros and Cons of Ab Initio Modelling
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Week 16
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239
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Summary of Structural Modelling - I
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240
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Summary of Structural Modelling - II
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241
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Summary of Structural Modelling - III
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242
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Review of Sequence Analysis
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243
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Review of Phylogenetics
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244
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Review of Protein Sequencing
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245
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Review of RNA Structure Prediction
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246
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Review of Protein Structures
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247
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Review of Homology Modelling
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248
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Conclusions from this Course
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249
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Advanced Follow-up Courses
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250
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Careers in Bioinformatics
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