Bioinformatic Methods I from Coursera

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 2023.

What's inside

Syllabus

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.

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.

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.

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

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.

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).

'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.

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

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Delves into bioinformatics, which is a key tool used by physicians, researchers, molecular biologists, and pharmaceutical scientists

Based on an upper-level undergraduate course, indicating the thoroughness of the material

Taught by experts in bioinformatics, Nicholas and Provart, who are recognized for their work in the field

Topics, such as sequence alignment and protein interaction networks, have extensive applications in drug discovery and development

Covers a wide range of techniques, from traditional sequence analysis to cutting-edge metagenomics

Provides hands-on experience through interactive labs and exercises

Reviews summary

Intro to bioinformatics methods

learners say this course is an engaging introduction to bioinformatics. Students new to bioinformatics may find this course a good starting point. It is largely positive with engaging assignments. The course is well-received by learners with many positive reviews. Reviews emphasize the excellent course structure with good pacing and topic order.

well organized and informative

"Excellent course to explore the basics and fundamentals for multiple bioinformatics data type analysis. Great job still updating it."

"This course is very helpful organized, easy to understand, and explained everything steps by step which will help to grasp the concept easily."

"The course is very interactive and informative, moreover I learned so many new skills because the explanation is done step by step and easy to understood."

hands-on, plenty of examples

"I truly recommend this course because in the labs you can practice all the theory you have learn and I really like the methodology ."

"Excellent course with good assignments for learning, I loved the hands on training to use various websites and tools for data analysis. "

"This is one of the most exciting & knowledge providing course, I did. Professor Provart explained all the things in detail & the labs were well-illustrated."

knowledgeable, clear explanations

"The teacher has a very good way of educating which made the course very accessible."

"Excellent teaching. Explanation before and after the laboratory was great help. Lab discussion after the lab really help us to solve if we have any dounts."

"Nicholas Provart is a great instructor!This course was very useful. I'll highly recommend other students to take this course."

can be challenging for beginners

"I am a biology student and found the course quite easy to follow, and the different databases which Prof Provart was very interesting and relevant to the work I wish to do in research. However, I have had friends (not from a science background) who took the course at the same time as I did but had to drop out because they could not follow the material - therefore the prerequisite of molecular biology is one that is necessary."

"The very last assignment wouldn't work for me, for the final question. Total bummer. I was doing everything according to instructions and even checking but it wouldn't work. Don't feel like explaining but the conversion to mega just was faulty, and the instructor's instructions to fix the problem didn't help either."

"Introductory videos could have been shortened with a video description of Lab work."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Bioinformatic Methods I with these activities:

Review basic biology concepts

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Refresh your understanding of basic biological principles to enhance your comprehension of the course material.

Browse courses on Biology

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Review your notes from previous biology courses.
Use online resources or textbooks to supplement your understanding.

Review NCBI and BLAST

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Learn to use NCBI for retrieving biological data and sequence information to prepare for the following modules.

Browse courses on NCBI

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Go to the NCBI website and explore its resources.
Use BLAST to search for similar sequences.

Practice using bioinformatics databases

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Enhance your proficiency in using bioinformatics databases to access and analyze biological data.

Browse courses on Data Analysis

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Identify different bioinformatics databases.
Practice searching and retrieving data from these databases.

Six other activities

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Show all nine activities

Multiple sequence alignment practice

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Practice multiple sequence alignment to improve understanding of sequence conservation and homology.

Browse courses on Multiple Sequence Alignment

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Use Clustal or MUSCLE to align a set of sequences.
Identify conserved and variable regions in the alignment.

Read Molecular Biology of the Cell

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Gain a comprehensive understanding of the fundamental principles of molecular biology and cell biology.

View Molecular Biology of the Cell on Amazon

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Read the book thoroughly.
Make notes and highlight important concepts.
Answer the review questions at the end of each chapter.

Follow tutorials on bioinformatics software

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Build your bioinformatics skills by working through tutorials on commonly used software.

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Identify tutorials for relevant bioinformatics software.
Follow the tutorials step-by-step.

Join a study group

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Discuss course materials, share notes, and work on assignments together to enhance understanding.

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Find other students taking the course and form a study group.
Meet regularly to discuss the material.
Work together on assignments.

Create a bioinformatics resource list

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Compile a list of useful bioinformatics resources to support your work during and after the course.

Browse courses on Databases

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Search for and evaluate different bioinformatics resources.
Create a list of resources, including their descriptions and links.

Contribute to an open-source bioinformatics project

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Gain hands-on experience with bioinformatics tools and contribute to the community.

Browse courses on Open Source

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Identify an open-source bioinformatics project that aligns with your interests.
Start contributing to the project by reporting bugs, writing documentation, or developing new features.

Career center

Learners who complete Bioinformatic Methods I will develop knowledge and skills that may be useful to these careers:

Molecular Biologist

A Molecular Biologist studies the structure and function of molecules in living organisms. This course may be useful for Molecular Biologists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Molecular Biologists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Microbiologist

A Microbiologist studies microorganisms, such as bacteria, fungi, and viruses. This course may be useful for Microbiologists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Microbiologists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Geneticist

A Geneticist studies the genes and chromosomes of living organisms. This course may be useful for Geneticists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Geneticists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Computational Biologist

A Computational Biologist uses computer science and mathematics to solve complex problems in biology and medicine. This course may be useful for Computational Biologists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Computational Biologists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Research Scientist

A Research Scientist conducts research to develop new products and technologies. This course may be useful for Research Scientists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Research Scientists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Physician

A Physician diagnoses and treats diseases. This course may be useful for Physicians as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Physicians can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Statistician

A Statistician collects, analyzes, and interprets data. This course may be useful for Statisticians as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Statisticians can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Software Engineer

A Software Engineer designs, develops, and maintains software applications. This course may be useful for Software Engineers as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Software Engineers can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Medical Scientist

A Medical Scientist conducts research to develop new treatments and cures for diseases. This course may be useful for Medical Scientists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Medical Scientists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Science Writer

A Science Writer writes about scientific topics for a general audience. This course may be useful for Science Writers as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Science Writers can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Technical Writer

A Technical Writer writes about technical topics for a specific audience. This course may be useful for Technical Writers as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Technical Writers can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Biostatistician

A Biostatistician develops new statistical and computational tools that can help researchers collect, analyze, and interpret biological data. This course may be useful for Biostatisticians as it introduces databases, sequence alignments, protein interaction networks, and other tools for analyzing biological data. By taking this course, Biostatisticians can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Teacher

A Teacher teaches students at a school or university. This course may be useful for Teachers as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Teachers can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Data Scientist

A Data Scientist collects, analyzes, and interprets data to help businesses make better decisions. This course may be useful for Data Scientists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Data Scientists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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Pharmacist

A Pharmacist dispenses medications and provides advice on their use. This course may be useful for Pharmacists as it introduces databases, sequence alignments, protein interaction networks, gene expression data analysis, and other tools for analyzing biological data. By taking this course, Pharmacists can build a foundation in bioinformatics and stay up-to-date on the latest bioinformatics techniques.

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