About this Course
Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful information pertaining to the system being studied. This course focuses on employing existing bioinformatic resources – mainly web-based programs and databases – to access the wealth of data to answer questions relevant to the average biologist, and is highly hands-on. Topics covered include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction networks, in two separate parts. The first part, Bioinformatic Methods I (this one), deals with databases, Blast, multiple sequence alignments, phylogenetics, selection analysis and metagenomics. This, the second part, Bioinformatic Methods II, covers motif searching, protein-protein interactions, structural bioinformatics, gene expression data analysis, and cis-element predictions. This pair of courses is useful to any student considering graduate school in the biological sciences, as well as students considering molecular medicine. Both provide an overview of the many different bioinformatic tools that are out there. These courses are based on one taught at the University of Toronto to upper-level undergraduates who have some understanding of basic molecular biology. If you're not familiar with this, something like https://learn.saylor.org/course/bio101 might be helpful. No programming is required for this course.
Globe

100% online course

Start instantly and learn at your own schedule.
Clock

Approx. 12 hours to complete

Suggested: 12-18 hours videos and labs
Comment Dots

English

Subtitles: English

Skills you will gain

Comparative GenomicsBioinformatics AnalysisGenomicsDna
Globe

100% online course

Start instantly and learn at your own schedule.
Clock

Approx. 12 hours to complete

Suggested: 12-18 hours videos and labs
Comment Dots

English

Subtitles: English

Syllabus - What you will learn from this course

1

Section
Clock
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. ...
Reading
4 videos (Total 52 min), 4 readings, 1 quiz
Video4 videos
Lecture25m
Lab Discussion24m
Summary0m
Reading4 readings
Acknowledgements10m
Course Logistics10m
Lecture Materials10m
Lab 1 -- Exploring NCBI30m
Quiz1 practice exercises
Lab 1 Quiz6m

2

Section
Clock
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....
Reading
4 videos (Total 58 min), 2 readings, 1 quiz
Video4 videos
Lecture32m
Lab Discussion23m
Summary0m
Reading2 readings
Lecture Materials10m
Lab 2 -- Advanced Blast and Comparative Genomics30m
Quiz1 practice exercises
Lab 2 Quiz6m

3

Section
Clock
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....
Reading
4 videos (Total 42 min), 2 readings, 1 quiz
Video4 videos
Lecture23m
Lab Discussion16m
Summary0m
Reading2 readings
Lecture Materials10m
Lab 3 -- Multiple Sequence Alignment30m
Quiz1 practice exercises
Lab 3 Quiz6m

4

Section
Clock
10 minutes to complete

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

...
Reading
1 quiz
Quiz1 practice exercises
Quiz: Modules 1-310m

5

Section
Clock
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....
Reading
4 videos (Total 36 min), 2 readings, 1 quiz
Video4 videos
Lecture25m
Lab Discussion9m
Summary0m
Reading2 readings
Lecture Materials10m
Lab 4 -- Phylogenetics30m
Quiz1 practice exercises
Lab 4 Quiz6m

6

Section
Clock
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)....
Reading
4 videos (Total 38 min), 2 readings, 1 quiz
Video4 videos
Lecture23m
Lab Discussion10m
Summary1m
Reading2 readings
Lecture Materials10m
Lab 5 -- Selection Analysis30m
Quiz1 practice exercises
Lab 5 Quiz6m

7

Section
Clock
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....
Reading
4 videos (Total 51 min), 2 readings, 1 quiz
Video4 videos
Lecture24m
Lab Discussion20m
Summary4m
Reading2 readings
Lecture Materials10m
Lab 6 -- Next Generation Sequencing Applications: RNA-Seq and Metagenomics30m
Quiz1 practice exercises
Lab 6 Quiz6m

8

Section
Clock
1 hour to complete

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

...
Reading
1 reading, 2 quizzes
Reading1 readings
Final Assignment Instructions10m
Quiz2 practice exercises
Review: Modules 5-710m
Final Assignment10m
4.7
Direction Signs

18%

started a new career after completing these courses
Briefcase

83%

got a tangible career benefit from this course
Money

25%

got a pay increase or promotion

Top Reviews

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

About University of Toronto

Established in 1827, the University of Toronto has one of the strongest research and teaching faculties in North America, presenting top students at all levels with an intellectual environment unmatched in depth and breadth on any other Canadian campus. ...

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