Course Overview
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Course Synopsis
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This course covers advanced topics in connection to Bioinformatics domain such as various bioinformatics databases various techniques to predict gene protein RNA structure. estimate local and global alignments and an introduction to drug discovery. This course further sheds light on state of the art applications of bioinformatics phylogenetic analysis homology modeling and detail discussion on Chou Fasman Algorithm.
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Course Learning Outcomes
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At the end of this course the students would be able to
- Understand genes and proteins at structural level using computational tools.
- Analyze and interpret structures and functions of genes RNA and proteins
- Understand genomic variants and enable them to analyzing impact of SNP on protein structure and function.
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Course Calendar
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Week 01
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1
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Applications of Bioinformatics-I
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2
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Applications of Bioinformatics-II
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3
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Nucleotide Sequence databases
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5
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Genome and organism specific databases
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6
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Gene expression databases
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10
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Protein Sequence Retrieval
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Week 02
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16
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Epichromosomal elements (EEs)
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18
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Transposable Elements (TEs)
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19
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Eukaryotic Gene Structure
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21
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Comparative Proteomics
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22
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Between proteome comparison
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23
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Horizontal Gene Transfer
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Week 03
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31
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Dynamic Programming II
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32
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Algorithm for Dynamic Programming
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34
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Restriction Mapping II
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35
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Partial Digest Problem
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36
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Practical Restriction Mapping Algorithm
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Week 04
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37
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Partial Digest Algorithm I
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38
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Partial Digest Algorithm II
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39
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Regulatory Motifs in DNA Sequences
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43
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Motif Finding Problem I
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44
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Motif Finding Problem II
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45
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Search Trees – Introduction
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46
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Search Trees – Best Alternative
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47
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Algorithm for Search Trees I
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48
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Algorithm for Search Trees II
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Week 05
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53
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Simple Motif Search Algorithm
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54
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Branch and bound Algorithm
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55
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Brute Force Median Search
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57
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A greedy approach to motif finding
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58
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The Power of DNA Sequence Comparison
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59
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Brute Force vs Greedy Algorithm
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Week 06
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65
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Longest Common Sequences I
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66
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Recurrence for LCS problem
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71
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Local Sequence Alignment I
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72
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Local Sequence Alignment II
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Week 07
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73
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Local Alignment Problem
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74
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Progressive Multiple Alignment
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77
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one Approach for Gene Prediction
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78
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Second Approach for Gene Prediction
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79
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Statistical Approach to Gene Prediction I
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80
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Statistical Approach to Gene Prediction II
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81
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Statistical Approach to Gene Prediction III
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82
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Similarity based Approached to Gene Prediction I
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83
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Similarity based Approached to Gene Prediction II
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Week 08
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87
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Prediction of Splice Junctions
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89
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Annotation of assembled Genome
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90
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Pattern Finding in a Genome
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91
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Pattern Finding Algorithms
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93
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Knuth-Morris-Pratt Algorithm
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Week 09
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98
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Optimal Alignment Methods
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99
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Needleman-Wunsch Algorithm
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100
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Smith-Waterman Algorithm
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104
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sequencing by hybridization
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105
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Fragment Assemly in DNA sequencing
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106
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Strategy for Sequencing
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107
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protein sequence and identification
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108
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computational protein sequencing
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Week 10
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109
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Mass spectrophotometry
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110
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The peptide sequencing problem 1
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111
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The peptide sequencing problem 11
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112
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protein identification via database search
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113
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Modified Protein Identification Problem
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114
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Protein Structure Prediction
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115
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Predicting Secondary Structures
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116
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Introduction to Chou Fasman Algorithm
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117
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2’ Structures in Chou Fasman Algorithm
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118
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Chou Fasman Algorithm - I
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119
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Chou Fasman Algorithm - II
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120
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Chou Fasman Algorithm - III
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Week 11
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121
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Chou Fasman Algorithm - IV
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122
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Chou Fasman Algorithm – Flowchart
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123
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Chou Fasman Algorithm – Flowchart II
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124
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Chou Fasman Algorithm – Flowchart III
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125
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Chou Fasman Algorithm – Improvements
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126
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Summary of Visualization, Classification and Prediction
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127
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Introduction to Homology modelling
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128
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Homology, Paralogy and Orthology
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129
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Workflow for Structural Modelling
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130
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Seven Steps to Homology Modelling - I
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131
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Seven Steps to Homology Modelling - II
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132
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Seven Steps to Homology Modelling - III
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Week 12
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133
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Seven Steps to Homology Modelling - IV
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134
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Seven Steps to Homology Modelling - V
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135
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Seven Steps to Homology Modelling - VI
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136
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Modeller for Homology Modelling
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137
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Fold Recognition/Threading I
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138
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Fold Recognition/Threading II
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139
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Fold Recognition/Threading III
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140
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Online Tools for Threading - iTasser
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141
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Advantages and Disadvantages of Threading
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142
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3D-1D Bowie Algorithm
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143
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Introduction to Ab-Initio Modelling
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144
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Rationale of Ab Initio Modelling
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Week 13
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145
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Strategies for Ab Initio Modelling
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146
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Energy States of Folded Proteins
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147
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Local versus Global Minima
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148
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Pros and Cons of Ab Initio Modelling
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149
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Summary of Structural Modelling - I
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150
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Summary of Structural Modelling - II
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151
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Summary of Structural Modelling - III
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152
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Review of Sequence Analysis
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153
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Review of Phylogenetics
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154
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Review of Protein Sequencing
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155
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Review of RNA Structure Prediction
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156
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Review of Protein Structures
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Week 14
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157
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Review of Homology Modelling
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158
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Conclusions from this Course
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159
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Advanced Follow-up Courses
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160
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Careers in Bioinformatics
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162
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RNA Secondary Structure
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163
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RNA Secondary Structure Prediction
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Week 15
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173
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Advantages of Bioinformatics in forensic
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174
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Methods used in DNA profiling
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176
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DNA profile generation
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177
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Introduction to Drug Discovery
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178
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Drug Discovery Applications
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180
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Pharmacogenetics applications
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Week 16
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181
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Drug Discovery Pipeline
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182
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Drug Discovery Methods
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185
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Steps for Creation of Biomedical Corpora
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186
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Target discovery strategy
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187
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Strategies To Identify Possible Drug Targets
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