Expected Preparations:

  Biomolecules:
The molecules of life; The genetic code; Nucleic acids; Amino acids; Protein folding; Post-translational modifications and protein biochemistry; Membrane proteins; Biological function.
   []
NA 		  [BIN]
Abstractions 		  [FND]
Genetic_code 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: The 20 amino acids and the one-letter code
Objectives:

This unit will …

  • introduce the concept of sequence as an abstraction and the common one-letter codes for DNA and amino acids that we use to realize it;

  • list the conventions we use when writing sequence;

  • discuss how amino acid properties relate to their function in a folded protein, and how this conditions which amino acid is found where in a sequence;

  • demonstrate R code to read, analyse and manipulate strings.

 Outcomes:

After working through this unit you …

  • can draw the structure formula of all 20 proteinogenic amino acids1 and assign them to categories like “small”, “charged” or “hydrophobic”;

  • can identify the coding sequence and frame for a DNA sequence that is labelled as “plus” or “minus”;

  • can competently read, analyse and manipulate strings in R;

  • can shuffle sequences (permute them) and create sequences with specific target ditributions of characters, in R.

Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.

Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don’t overlook these.

Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Evaluation:

NA: This unit is not evaluated for course marks.

Contents

Sequence is the most fundamental concept to abstract biomolecules for computational purposes. In this unit we discuss some of the implications and conventions, and explore handling and processing character vectors and strings in R.

Task…

 

Task…

  • Open RStudio and load the ABC-units R project. If you have loaded it before, choose File ▸ Recent projects ▸ ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
  • Choose Tools ▸ Version Control ▸ Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included. This ensures that your data and code remain up to date when we update, or fix bugs.
  • Type init() if requested.
  • Open the file BIN-Sequence.R and follow the instructions.

     

    Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.

 

Review

Further Reading

Amino acids (Wikipedia) - use this to review and memorize: structural formula, one-letter code, charge, relative size, and polarity for the 20 proteinogenic amino acids.

The “sense” of how nucleotide sequences are written (Wikipedia)

Introduction to the **stringr** package

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-Sequence

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.1
Version History:
–  1.1 2020 Updates
–  1.0 First live version
–  0.1 First stub
Tagged with:
–  Unit
–  Live
–  Has lecture slides
–  Links to R course project
–  Has review questions
–  Has further reading

 

[END]

  1. Technically there are 21 proteinogenic amino acids, because some proteins contain Selenocysteine(W) translated from TGA codons. However this is not universal, and thus Sec is as much a proteinogenic amino acid as Pluto is not a planet. Technically correct. The memnonic for the Sec one-letter code U is: u as in PlUto.↩︎