BIN-Sequence

Sequence

 

Keywords:  The 20 amino acids and the one-letter code

 

 

 

Abstract

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.

 

This unit ...

Prerequisites

You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

• Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.

You need to complete the following units before beginning this one:

• You are expected to know the names, structures and (bio)chemical properties of the 20 proteinogenic amino acids;
• BIN-Abstractions (Abstractions for Bioinformatics)
• FND-Genetic_code (Genetic 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 acids 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 competent 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.

 

Contents

Task:

• Read the introductory notes on the concept of biomolecular "sequence".

 

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.
• 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.

 

 

 

Further reading, links and resources

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

 

Notes

 

Self-evaluation

• Answer the questions on amino acids from 2002 - 2009 BCH441 Final Exam questions.

 

 

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If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-09-28

Version:

1.0

Version history:

• 1.0 First live version
• 0.1 First stub

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