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Learn Bioinformatics

Overview

This list consists of ~10 tutorials to learn bioinformatics. You can think of this list as a "Free Online Nano Book". We'll cover important bioinformatics topics, learning (a) the biological significance of each problem, and (b) the computational algorithms used to solve the problem. Everything is 100% free.

What is Bioinformatics?

What is a DNA? What is a Protein?

This section (single tutorial) provides the biological context for the rest of this course. It describes what DNAs and proteins are, and how we can model them as a sequence of characters.

DNA and Protein: What they are, and what role do they play?
Free
11 mins

Conserved Sequences and Regulatory Motifs with Brute-Force Algorithms and Randomized Algorithms

Conserver sequences and regulatory motifs are short sequences (say of length 15-30) which occur frequency in the genome. These sequences serve a variety of functions - such as regulating gene expression (and hence how much of a protein is produced) and indicating where genes begin. We'll see how to find these sequences using brute-force algorithms and randomized algorithms.

Genome Assembly and Sequence Alignment with Graph Algorithms and Dynamic Programming

Recently, we've figured out cost effective ways of sequencing a human genome, i.e. taking a human genome and reading sequence of 3-4 billion nucleic acids (A, C, G and T) that it comprises of. In this section, we'll see how this is achieved. We'll also see how we can find similar regions in two different genomes, which allows us to do things like infer evolutionary history and predict protein function.

Start this course

DNA and Protein: What they are, and what role do they play?

Category: Machine Learning

1 Comment

Top comment in this discussion

Martins Nkume9w

I am delighted to begin this course.

Problem Formulation

In SVM, the decision function for predicting data points x corresponds to the equation of an hyperplane:

f_w(x) = w^T x + w_0

Sequence Motifs and their Biological Significance

Sequence motifs are nucleic acid sequences that are widespread across or within a genomes and have or are speculated to have certain regulatory or structural biological functions.

Motifs that are found in different parts of the genomes like exons, introns and junk, have different functions. Motifs present in the exons ( coding part of the genome) decide the structure of the protein or label proteins to be sent to certain parts of the cell for processes like phosphorylation. Motifs that are present in introns (which makes up the non coding part of genome) are usually the regulatory sequences which determine the amount of gene expression and binding sites of proteins. Satellite DNA, which is the main component of centromeres and heterochromatin, is an example of motif found in junk parts of the genome.

Sequence Motifs and Consensus Se...

Dropout algorithm

Dropout is a regularization technique where during each iteration of gradient descent, we drop a set of neurons selected at random. By drop, what we mean is that we essentially act as if they do not exist.