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USMx: BIF001x DNA Sequences: Alignments and Analysis

                                                         

Syllabus

DNA Sequences: Alignments and Analysis

Course Dates: August 21 – October 16

Course Description

Gene sequences and the rest of the genome play an important role in determining how an organism functions normally and reacts when situations change. DNA sequences can also be used to determine relationships between organisms and form the underpinnings of the Tree of Life.

Since DNA sequences play such an important role in any organism it should not be surprising that any changes to a sequence could lead to alterations in behavior or response. For example, a small number of specific changes in DNA sequence have been shown to lead to tumor development in mammals or the production of enzymes with altered properties.

One of the jobs of a bioinformatician is to help determine where these changes are in a DNA sequence and sort out in that context what effects may result, which is usually done by aligning the sequences in question.

Course Learning Outcomes

In this course, part of the Bioinformatics MicroMasters program, you will learn to: 

  • Synthesize and analyze biological big data.
  • Apply the most popular sequencing algorithms and learn how they function.
  • Develop a comprehensive knowledge of the history of bioinformatics and its place among the biological sciences.
  • Perform database searches to determine the possible function of unknown DNA sequences.
  • Gain exposure to the analysis of gene expression data from microarrays and Next Generation
  • sequencing technologies.
  • Learn the most common approaches and methods for sequencing whole genomes and comparing them.
  • Apply and learn about the most common phylogenetic algorithms.

Course Information

This is a self-paced online course.  All course materials are presented in English.

Learners new to edX are recommended to take the DemoX course, which is designed to show new students how to take a course on edx.org. 

Course Materials

All materials are freely available within the course. Additional references, resources, and optional readings can be easily accessed and downloaded from the References, Resources, and Optional Readings sections of this course.

Course Schedule

This is a self-paced course, as such, all content (e.g. weekly knowledge checks, discussions, assessments ) will be available starting in Week 1 and will remain available through the entire eight weeks of the course.

Students should plan to spend between 4-6 hours each week to fully complete each module.

Week

Topics

Suggested Reading

Activities

1

·      Origins and History

·      Main Sub-disciplines of Bioinformatics

·      Molecular Biology Review

 

 

·      Week 1 Discussion

·      Week 1 Knowledge Check

2

·      Nucleic Acid Sequencing

·      PCR

·      Genome Sequencing

·      Sequencing Databases

 

Chapter 8 in Exploring Bioinformatics

·      Week 2 Discussion

·      Week 2 Knowledge Check

3

·      Pairwise Alignments

·      Brute Force/Dot Matrix/Dynamic Programming

·      Needleman-Wunsch/Smith-Waterman

 

Chapter 3 in Exploring Bioinformatics

·      Week 3 Discussion

·      Week 3 Knowledge Check

4

·      Heuristic Methods

·      Multiple Sequence Alignments

 

Chapter 4 in Exploring Bioinformatics

·      Week 4 Discussion

·      Week 4 Knowledge Check

·      Mid Term Assessment

 

5

·      History of Phylogenetics

·      Modern Phylogenetics methods

·      How to construct a Phylogenetic tree

·      Types of Phylogenetic trees

 

Chapter 5 in Exploring Bioinformatics

·      Week 5 Discussion

·      Week 5 Knowledge Check

6

·      Genome Organization and Regulation

·      Types of Pattern Finding Methods

 

Chapter 9 and 10 in Exploring Bioinformatics

·      Week 6 Discussion

·      Week 6 Knowledge Check

7

·      Gene Expression

·      Detecting Gene Expression

·      Data Analysis Techniques

 

Chapter 7 in Exploring Bioinformatics

·      Week 7 Discussion

·      Week 7 Knowledge Check

8

·      Comparative Genomics

·      Synteny

 

·      Week 8 Discussion

·      Week 8 Knowledge Check

·      Final Assessment

Course Grading and Policy

You will be able to view all material and take any knowledge checks, or participate in discussions at any time during the course. However, to be awarded a certificate you will need to have completed all the assessments, discussions and knowledge checks by the last scheduled date for the course. 

The course score for BIF 001x is determined from two components: a Mid Term Assessment (50%) and a Final Assessment (50%).

Mid-Term Assessment - At the end of the material for Week 4, there is Mid-Term assessment, which accounts for 50% of your overall score in the course.  The Mid-Term contains 25 randomly generated questions based on the topics covered from Week 1 to 4. These questions are multiple choice and are two points each.  Note: you will only have one attempt at this assessment.

Final Assessment - At the end of the material for Week 8, there is a Final assessment, which accounts for 50% of your overall score in the course. The Final assessment contains 25 randomly generated questions based on the topics covered from Week 5 to 8.  These questions are multiple choice and are two points each.  Note: you will only have one attempt at this assessment.

Certification

For those students working to obtain the MicroMasters certificate, you must register for the verified track before the deadline and obtain a total score of 80% or greater in the class. 

For those verified students who receive an edX certificate, it will appear on their edX dashboard after the course ends. As of December 7, 2015, edX no longer offers certificates for students who audit a course.