About this Course
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Beginner Level

Approx. 13 hours to complete

Suggested: 12-18 hours videos and labs...

English

Subtitles: English

Skills you will gain

Genetic AnalysisBioinformatics AnalysisEvolutionComparative Genomics

100% online

Start instantly and learn at your own schedule.

Flexible deadlines

Reset deadlines in accordance to your schedule.

Beginner Level

Approx. 13 hours to complete

Suggested: 12-18 hours videos and labs...

English

Subtitles: English

Syllabus - What you will learn from this course

Week
1
3 hours to complete

NCBI/Blast I

In this module we'll be exploring the amazing resources available at NCBI, the National Centre for Biotechnology Information, run by the National Library of Medicine in the USA. We'll also be doing a Blast search to find similar sequences in the enormous NR sequence database. We can use similar sequences to infer homology, which is the primary predictor of gene or protein function.

...
4 videos (Total 52 min), 4 readings, 1 quiz
4 videos
Lecture25m
Lab Discussion24m
Summary
4 readings
Acknowledgements10m
Course Logistics10m
Lecture Materials10m
Lab 1 -- Exploring NCBI1h 30m
1 practice exercise
Lab 1 Quiz6m
Week
2
3 hours to complete

Blast II/Comparative Genomics

In this module we'll continue exploring the incredible resources available at NCBI, the National Centre for Biotechnology Information. We will be performing several different kinds of Blast searches: BlastP, PSI-Blast, and Translated Blast. We can use similar sequences identified by such methods to infer homology, which is the primary predictor of gene or protein function. We'll also be comparing parts of the genomes of a couple of different species, to see how similar they are.

...
4 videos (Total 58 min), 2 readings, 1 quiz
4 videos
Lecture32m
Lab Discussion23m
Summary
2 readings
Lecture Materials10m
Lab 2 -- Advanced Blast and Comparative Genomics1h 30m
1 practice exercise
Lab 2 Quiz6m
Week
3
2 hours to complete

Multiple Sequence Alignments

In this module we'll be doing multiple sequence alignments with Clustal (as implemented in MEGA), DiAlign, and MAFFT. Multiple sequences alignments can tell you where in a sequence the conserved and variable regions are, which is important for understanding the biology of the sequences under investigation. It also has practical applications, such as being able to design PCR primers that will amplify sequences from a number of different species, for example.

...
4 videos (Total 42 min), 2 readings, 1 quiz
4 videos
Lecture23m
Lab Discussion16m
Summary
2 readings
Lecture Materials10m
Lab 3 -- Multiple Sequence Alignment1h 30m
1 practice exercise
Lab 3 Quiz6m
Week
4
10 minutes to complete

Review: NCBI/Blast I, Blast II/Comparative Genetics, and Multiple Sequence Alignments

...
1 quiz
1 practice exercise
Quiz: Modules 1-310m
Week
5
2 hours to complete

Phylogenetics

In this module we'll be using the multiple sequence alignments we generated last lab to do some phylogenetic analyses with both neighbour-joining and maximum likelihood methods. The tree-like structure generated by such analyses tells us how closely sequences are related one to another, and suggests when in evolutionary time a speciation or gene duplication event occurred.

...
4 videos (Total 36 min), 2 readings, 1 quiz
4 videos
Lecture25m
Lab Discussion9m
Summary
2 readings
Lecture Materials10m
Lab 4 -- Phylogenetics1h 30m
1 practice exercise
Lab 4 Quiz6m
Week
6
2 hours to complete

Selection Analysis

In this module we'll take a set of orthologous sequences from bacteria and use DataMonkey to analyze them for the presence of certain sites under positive, negative or neutral selection. Such an analysis can help understand the biology of a set of protein coding sequences by identifying residues that might be important for biological function (those residues under negative selection) or those that might be involved in response to external influences, such as drugs, pathogens or other factors (residues under positive selection).

...
4 videos (Total 38 min), 2 readings, 1 quiz
4 videos
Lecture23m
Lab Discussion10m
Summary1m
2 readings
Lecture Materials10m
Lab 5 -- Selection Analysis1h 30m
1 practice exercise
Lab 5 Quiz6m
Week
7
3 hours to complete

'Next Gen' Sequence Analysis (RNA-Seq) / Metagenomics

In this module we'll explore some of the data that have been generated as a result of the rapid decrease in the cost of sequencing DNA. We'll be exploring a couple of RNA-Seq data sets that can tell us where any given gene is expressed, and also how that gene might be alternatively spliced. We'll also be looking at a couple of metagenome data sets that can tell us about the kinds of species (especially microbial species that might otherwise be hard to culture) that are in a given environmental niche.

...
4 videos (Total 51 min), 2 readings, 1 quiz
4 videos
Lecture24m
Lab Discussion20m
Summary4m
2 readings
Lecture Materials10m
Lab 6 -- Next Generation Sequencing Applications: RNA-Seq and Metagenomics1h 30m
1 practice exercise
Lab 6 Quiz6m
Week
8
1 hour to complete

Review: Phylogenetics, Selection Analysis, and 'Next Gen' Sequence Analysis (RNA-seq)/Metagenomics + Final Assignment

...
1 reading, 2 quizzes
1 reading
Final Assignment Instructions10m
2 practice exercises
Review: Modules 5-710m
Final Assignment10m
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Top reviews from Bioinformatic Methods I

By EDApr 27th 2017

Great course. All lectures provide a biological context for the tools you learn in the labs. The labs themselves provide a great introduction to the many tools available for bioinformatic analysis.

By FJFeb 6th 2017

The videos were very clear on how to use various bioinformatic tools. I found no difficulty in understanding them. Really enjoyed the course. Looking forward to the next part of this course!

Instructor

Avatar

Nicholas James Provart

Professor
Cell & Systems Biology

About University of Toronto

Established in 1827, the University of Toronto is one of the world’s leading universities, renowned for its excellence in teaching, research, innovation and entrepreneurship, as well as its impact on economic prosperity and social well-being around the globe. ...

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