Bioinformatics Algorithms (Stepik)

Bioinformatics Algorithms (Stepik)
Free Course
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The course is aimed at students involved in computer science, biology or any other related field.
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Bioinformatics Algorithms (Stepik)
Explore the power of computing in modern biology and apply existing software tools to find recurring biological motifs within genes that are responsible for helping Mycobacterium tuberculosis go "dormant" within a host for many years before causing an active infection.

In the course, we investigate DNA replication, and ask the question, where in the genome does DNA replication begin? We will see that we can answer this question for many bacteria using only some straightforward algorithms to look for hidden messages in the genome.




Course content


Where in the Genome Does DNA Replication Begin?

A Journey of a Thousand Miles. . .

Hidden Messages in the Replication Origin

Some Hidden Messages are More Surprising than Others

An Explosion of Hidden Messages

The Simplest Way to Replicate DNA

Asymmetry of Replication

Peculiar Statistics of the Forward and Reverse Half-Strands

Some Hidden Messages are More Elusive than Others

A Final Attempt at Finding DnaA Boxes in E. coli

Epilogue: Complications in ori Predictions

CS: The Frequency Array

CS: Converting Patterns to Numbers and Vice-Versa

CS: Finding Frequent Words by Sorting

CS: Solving the Clump Finding Problem

CS: Solving the Frequent Words with Mismatches Problem

CS: Generating the Neighborhood of a String

CS: Finding Frequent Words with Mismatches 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