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Bioinformatics Algorithms

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Before Getting Started

Introduction to the Course

Where in the Genome Does DNA Replication Begin?

A Journey of a Thousand Miles The Finding Origin of Replication Problem DnaA Boxes The Hidden Message Problem Counting Words Coding Challenge: Implement Pattern Count The Frequent Words Problem Some Hidden Messages are More Surprising than Others Coding Challenge: Implement Pattern Matching An Explosion of Hidden Messages The Simplest Way to Replicate DNA Asymmetry of Replication Peculiar Statistics of the Forward and Reverse Half-Strands Deamination The Skew Diagram Coding Challenge: Implement Minimum Skew Some Hidden Messages are More Elusive than Others A Final Attempt at Finding DnaA Boxes in E. coli Epilogue: Complications in ori Predictions Quiz

DNA Replication: Open Problems, Charging Stations, and Detours

Open Problem: Multiple Replication Origins in a Bacterial Genome Open Problem: Finding Replication Origins in Archaea Open Problem: Finding Replication Origins in Yeast Open Problem: Computing Probabilities of Patterns in a String Charging Station: The Frequency Array Charging Station: Conversions between Patterns and Numbers Charging Station: Finding Frequent Words by Sorting Charging Station: Solving the Clump Finding Problem Charging Station: Solving Frequent Words with Mismatches Problem Charging Station: Generating the Neighborhood of a String Charging Station: Find Frequent Words with Mismatching by Sorting Detour : Big-O Notation Detour: Probabilities of Patterns in a String Detour: The Most Beautiful Experiment in Biology Detour: Directionality of DNA Strands Detour: The Towers of Hanoi Detour: The Overlapping Words Paradox

How Do We Assemble Genomes?

Exploding Newspapers The String Reconstruction Problem String Reconstruction With Overlap Graph: From String To Graph String Reconstruction With Overlap Graph: The Genome Vanishes String Reconstruction with Overlap Graph: Graph Representation String Reconstruction with Overlap Graph: Hamiltonian Paths String Reconstruction with Gluing Nodes and De Bruijn Graphs Walking in the de Bruijn Graph De Bruijn Graphs: Another Way of Construction De Bruijn Graphs: Construction from K-mer Composition De Bruijn graphs: Comparison with Overlap Graphs The Seven Bridges of Königsberg Euler’s Theorem Constructing Eulerian Cycles and Paths from Euler’s Theorem Constructing Universal Strings Assembling Genomes: From Reads to Read-Pairs Assembling genomes: Transforming Read-Pairs to Long Virtual Reads Assembling genomes: From Composition to Paired Composition Assembling genomes: Paired De Bruijn Graphs Epilogue: Genome Assembly Faces Real Sequencing Data Quiz

Assemble Genomes: Charging Stations, and Detours

Charging Station: The Effect Of Gluing On the Adjacency Matrix Charging Station: Generating All Eulerian Cycles Charging Station: Reconstructing String in Paired De Bruijn Graph Charging Station: Maximal Non-Branching Paths in a Graph Detour: A Short History of DNA Sequencing Technologies Detour: Repeats in the Human Genome Detour: Graphs Detour: The Icosian Game Detour: Tractable and Intractable Problems Detour: From Euler to Hamilton to de Bruijn Detour: Pitfalls of Assembling Double-Stranded DNA Detour: The BEST Theorem

How Do We Compare Biological Sequences?

The Discovery of Antibiotics

How Do Bacteria Make Antibiotics?

Where is Tyrocidine Encoded in the Bacillus Brevis Genome?

Dodging the Central Dogma of Molecular Biology

Cracking the Non-Ribosomal Code

From Protein Comparison to Non-Ribosomal Code

What do Oncogenes and Growth Factors Have in Common?

Introduction to Sequence Alignment

Sequence Alignment and the Longest Common Subsequence

The Manhattan Tourist Problem

Sightseeing in an Arbitrary Directed Graph

Sequence Alignment is the Manhattan Tourist Problem in Disguise

Making a case for Dynamic Programming: The Change Problem

Changing Money Recursively

Changing Money Using Dynamic Programming

The Manhattan Tourist Problem Revisited

From Manhattan to an Arbitrary Directed Acyclic Graph

Backtracking in the Alignment Graph

Scoring Alignments

From Global to Local Alignment

The Changing Faces of Sequence Alignment

The Changing Faces of Sequence Alignment: Fitting Alignment

The Changing Faces of Sequence Alignment: Overlap Alignment

Penalizing Insertions and Deletions in Sequence Alignment

Space Efficient Sequence Alignment

Epilogue: Multiple Sequence Alignment

Biological Sequences: Detours

Detour: Fireflies and the Non-Ribosomal Code Detour: Finding a Longest Common Subsequence Detour: Constructing a Topological Ordering Detour: PAM Scoring Matrices Detour: Divide-and-Conquer Algorithms Detour: Scoring Multiple Alignments

Conclusion

Scoring Alignments

Explore what scoring matrices are and what is wrong with the LCS scoring model.

What is wrong with the LCS scoring model?

Recall Marahiel’s alignment of the A-domains coding for Asp and Orn, which had 19 + 10 matches:

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