Bioinformatics Education and Tutorials
When we understand genetic sequences DNA, RNA and protein, plus how they relate to each other, how DNA acts as an information database on how to build all living things, we can start to ask deeper questions about a heritage, infections, allergy, diseases in general, genetic mutations, relationship of all species, how to increase food crop yield, how to design personalised medicine, tailor make genes and so on. The list is long.
The tutorials emphasize the underlying fundamental principles and ideas instead of first focusing on many details. The understanding of the concepts is the key to the learning process. One can always look up the details anytime, besides we would not remember all of them either.
Each tutorial is a self-contained entity. Because bioinformatics is a cross-disciplinary field, we have included pointers to relevant Biology and Biomedicine sections, e.g., such as immunology, microbiology, virology, genetics, infectious diseases and population biology.
Furthermore, each tutorial includes a list of prerequisites with links to those sections. Last but not least, many tutorials contain a wealth of images, animations or videos as required to enhance the learning experience and make it enjoyable.
The best part of it is that you can use the material for free for any non-commercial purpose. Go ahead and explore!
Don’t forget to study the history also! Why? Learn. To both study and value, the steps pioneers daringly took to where no one has gone before, to open new doors. Doors to brand new places for others to explore. To change the world for generations to come.
History from the 19th century to the 21st century. From Mendel and Miescher to the birth of bioinformatics and the completion of the human genome. The bold steps taken by great scientists to the unknown.
A starter level primer introduces the ideas of a match, mismatch, gap, insertion, deletion, indel, global and local alignments.
A basic level tutorial, introducing DNA and protein sequence alignments, substitution matrices and discusses the bases of sequence similarity.
An intermediate level tutorial, introducing pair-wise global (Needleman-Wunch) and local (Smith-Waterman) sequence alignment methods without advanced mathematics and discusses the main implementation aspects.
An intermediate level tutorial of BLOSUM and PAM substitution matrices describe their detailed, step by step construction.
Detailed step-by-step instructions on how to construct DNA scoring matrices and how to optimize them to target different sequence similarity levels. After this tutorial, you can design your DNA scoring matrices.
A comprehensive tutorial explains the effects of selection of scoring matrices for pair-wise sequence alignments and database searches. This tutorial also explores the impact of a 'wrong' scoring matrix selection and how all scoring schemes have explicit or implicit optimal target similarity.
This tutorial is an intermediate level tutorial on homology. We cover homology classes, hierarchies, analogous processes, and the concept of deep homology, among others.
A basic level tutorial describes what information and entropy is. Detailed step-by-step instructions on how to calculate information and entropy content for DNA and protein sequences. A basic introduction to sequence logos and their relation to information contained in multiple sequence alignments.
Currently working on this tutorial. I am planning to complete this by the end of the next week.
Although I wrote this a long time ago, the article provides a fascinating insight into the era when the International Human Genome Sequencing Consortium and Celera Genomics reported the drafts of the human genome project and later completed by April 2003.
A starter-level tutorial. It introduces the essential principles of hows and whys of the sequence assembly.
A sequence assembly can go wrong in many ways. Thus, we must assess both the correctness and completeness of an assembly. We go through the most common assembly quality metrics. N50, k-mers, and BUSCO.
In this practical, we learn the intricacies of assembling a ~5 Mb haploid genome using long read PacBio sequencing technology.
Genome is the blueprint of life.
"The creative process moves through five stages. It begins with preparation–an analytical time when the basic information or skills are assembled. It continues on to incubation–a more intuitive and subconscious time in which you connect the dots in a default state. If you stick with it through perspiration, this process will eventually lead to revelation–the eureka experience when you literally feel the tumblers of your mind click into place and you say: ‘A-ha, I have found the solution!’ The creative process ends with production, a time when the insights are put into a useful form and shared with others." View Source