This course is part of the Plant Bioinformatic Methods Specialization

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Nicholas James Provart

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Plant Bioinformatic Methods SpecializationUniversity of Toronto

About this Course

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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. 

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. 

Bioinformatic Methods I is regularly updated, and was completely updated for January 2021.

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Course 1 of 4 in the

Plant Bioinformatic Methods Specialization

Beginner Level

Approx. 20 hours to complete

English

Subtitles: English

Skills you will gain

Genetic AnalysisBioinformatics AnalysisEvolutionComparative Genomics

Flexible deadlines

Reset deadlines in accordance to your schedule.

Shareable Certificate

Earn a Certificate upon completion

100% online

Start instantly and learn at your own schedule.

Course 1 of 4 in the

Plant Bioinformatic Methods Specialization

Beginner Level

Approx. 20 hours to complete

English

Subtitles: English

Instructor

Instructor rating

4.74/5 (278 Ratings)

Nicholas James Provart

Professor

Cell & Systems Biology

102,807 Learners

4 Courses

Offered by

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.

Syllabus - What you will learn from this course

Content Rating98%(8,462 ratings)

Week

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.

3 hours to complete

4 videos (Total 52 min), 4 readings, 1 quiz

Week

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.

3 hours to complete

4 videos (Total 58 min), 2 readings, 1 quiz

Week

Week 3

3 hours to complete

Multiple Sequence Alignments

In this module we'll be doing multiple sequence alignments with Clustal and MUSCLE (as implemented in MEGA), 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.

3 hours to complete

4 videos (Total 46 min), 2 readings, 1 quiz

Week

Week 4

1 hour to complete

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

1 hour to complete

Week

Week 5

3 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.

3 hours to complete

4 videos (Total 43 min), 2 readings, 1 quiz

Week

Week 6

3 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).

3 hours to complete

4 videos (Total 39 min), 2 readings, 1 quiz

Week

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.

3 hours to complete

4 videos (Total 52 min), 2 readings, 1 quiz

Week

Week 8

1 hour to complete

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

1 hour to complete

1 reading

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TOP REVIEWS FROM BIOINFORMATIC METHODS I

by SAJul 11, 2020

This course is very well organized, easy to understand, and explained everything steps by step which will help to grasp the concept easily. If you are a beginner like me, you should take this course.

by EDApr 26, 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 5, 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!

by RGNov 4, 2017

I enjoyed doing the course. It is exciting to see how much one can learn from a few gene or protein sequences. Thank you for making the course understandable to a beginner in bioinformatics!

View all reviews

About the Plant Bioinformatic Methods Specialization

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply and in a high-throughput manner. These data sets in turn allow us to generate hypotheses at the click of a mouse or tap of a finger.The Plant Bioinformatics Specialization on Coursera introduces core bioinformatic competencies and resources, such as NCBI's Genbank, Blast, multiple sequence alignments, phylogenetics in Bioinformatic Methods I, followed by protein-protein interaction, structural bioinformatics and RNA-seq analysis in Bioinformatic Methods II. In Plant Bioinformatics we cover 33 plant-specific online tools from genome browsers to transcriptomic data mining to promoter/network analyses and others. Last, a Plant Bioinformatics Capstone uses these tools to hypothesize a biological role for a gene of unknown function, summarized in a written lab report.This specialization is useful to any modern plant molecular biologist wanting to get a feeling for the incredible scope of data available to researchers. A small amount of R programming is introduced in Bioinformatic Methods II, but most of the tools are web applications. It is recommended that you have access to a laptop or desktop computer for running these as they may not work as mobile applications on your phone or tablet.

Frequently Asked Questions

When will I have access to the lectures and assignments?
Access to lectures and assignments depends on your type of enrollment. If you take a course in audit mode, you will be able to see most course materials for free. To access graded assignments and to earn a Certificate, you will need to purchase the Certificate experience, during or after your audit. If you don't see the audit option:
The course may not offer an audit option. You can try a Free Trial instead, or apply for Financial Aid.
The course may offer 'Full Course, No Certificate' instead. This option lets you see all course materials, submit required assessments, and get a final grade. This also means that you will not be able to purchase a Certificate experience.
What will I get if I subscribe to this Specialization?
When you enroll in the course, you get access to all of the courses in the Specialization, and you earn a certificate when you complete the work. Your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.
Is financial aid available?
Yes, Coursera provides financial aid to learners who cannot afford the fee. Apply for it by clicking on the Financial Aid link beneath the "Enroll" button on the left. You'll be prompted to complete an application and will be notified if you are approved. You'll need to complete this step for each course in the Specialization, including the Capstone Project. Learn more.

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Bioinformatic Methods I

About this Course

Skills you will gain