
There are several things that you need to know before you start the course. In this lecture I will explain to you about the course structure and contents as well as the learning outcomes that you will gain from this course.
We will look into several phases of scientific development and growth until to the advent of Bioinformatics which accelerated the advancement of biotechnology research.
This is just a refresher topic for those who are familiar with the central dogma of molecular biology. For those of you are not from the biotechnology background, this could be something new.
Learning basic analysis will definitely help you to understand better in doing advanced Bioinformatics works. Here I will briefly explain about the current analysis trends in Bioinformatics.
In order to fully understand what database is, it is important to know the purpose and the structure of a database. Since it is a computer system that stores information, it is ideal to know why we need a database in scientific research.
Here in this section we will look specifically into GenBank and some other nucleotide databases. I will teach you on how to perform a query from GenBank.
Nucleotide databases are not the only type of databases you will learn. I will also introduce to you on the protein databases. pay a closer attention on this section as we will be covering a specific chapter on Proteomics alone later on.
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.
Let's try to align two nucleotide sequences together and observe how many types of alignment we can get and then decide which one is the best alignment. In this section, I will explain to you on just that alone.
There are two methods to perform a sequence alignment - local and global sequence alignments. In this section you will learn how to construct both local and global sequence alignment matrices in order to understand how alignment algorithm works.
In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences.
A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences
In this section, I have provided the installer for Mega version 6, a zipped folder containing the FASTA sequence file for Ruminants, and the User Manual on how to perform the phylogenetic tree construction using Mega 6. All you need to do is to follow through the User Manual. The download links are as below. If you have any question, do share with me through the comment box. Thank you.
It's WORTH your money! This program runs through 6 chapters. This is a self-paced course that suits to your own daily busy schedules. Self-paced gives you the freedom to complete each topic based on your own available time before proceeding to the next chapter without hurry. Basically, I will teach about 6 fundamental topics in Bioinformatics to you. Just to let you know, I don't intend to cover a basic programming class here. Udemy has a lot of great programming courses that can be applied in a Bioinformatics settings. So please well equip yourself with at least Python, Perl, PHP, Java, SQL and R programming. That will really help you to take off faster as a Bioinformatician in the near future. In 6 days you will learn through video lectures and tutorials about:
Day 1 - Introduction to Bioinformatics
We will start this course with a brief definition of Bioinformatics - what exactly it constitutes of, and the importance of this field in the scientific world. Also, I will share with you the history of how Bioinformatics came into being - the reason why it was coined.
Day 2 - Bioinformatics Databases
One of the reasons why Bioinformatics exists is due to the increased amount of biological datasets. These are huge scientific research outputs that need to be managed. In this chapter you will learn first of all how data is stored and manipulated. Subsequently I will begin to introduce to you about nucleotide databases. Bioinformatics is all about managing data and providing scientific knowledge. In this chapter we will also focus on protein databases. These two types of databases compliment each other and both are important for your studies. An example of database that we will be covering here is UniProt.
Day 3 - Sequence Alignment
This is one of my favorite chapters. Have you ever wonder how two sequences are being compared using two different sequence alignment algorithms? Think about aligning 100 DNA sequences at one time - is there a way to perform the multiple sequence alignment? In this chapter I will teach you how to perform Global and Local sequence alignments - it's all about basic concepts of scoring matrices. Let's get serious with Bioinformatics from here onward!
Day 4 - BLAST programs
Yeaps! Also my favorite! I will teach you how to perform a Local sequence alignment using a Bioinformatics tool known as BLAST (Basic Local Alignment Search Tool). We will look into both nucleotide and protein sequence BLAST programs and learn how to read and interpret BLAST results in-details.
Day 5 - Molecular Phylogenetics
Let's get straight to the point. You are uniquely different and special! If you are a big fan of X-Men and other Sci-Fi Hollywood movies talking about aliens, superhuman, man with extraordinary powers, or even just about how diversified we are - this is the time to pay attention to this module. I will teach you about how species is identified and classified using genetic data. To do that we will also be looking into several types of phylogeny analysis algorithms and construct a tree of life from a specific set of sequences. Don't skip this session!
Day 6 - Genome Analysis
In this module you will learn about a genome. We will look closely into both structural and comparative genomics. The detail parts begin with the sequencing technologies and followed with genome assembly and annotation.
I have prepared several sets of quizzes and assignments for you to solve. Based
on previous experiences with other students, I am aware that some of
you might need a one-to-one discussion therefore you are
welcome to request for an online meeting / discussion session with me.
Just to help you progress in this course. By the way, the first chapter is F.O.C. for preview! Register now to start learning about what Bioinformatics can do to help you, be it in research routines or for career development or simply just for personal interest. You have a lifetime access to this course and the course materials will be updated periodically. Do check for updates from time to time.