Difference between revisions of "BIN-Sequence"

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Sequence
 
Sequence
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(The 20 amino acids and the one-letter code)
 
(The 20 amino acids and the one-letter code)
 
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<b>Abstract:</b><br />
 
<b>Abstract:</b><br />
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*<b>Time management</b>: 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.
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<li><b>Time management</b>: 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.</li>
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
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<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 
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<b>Prerequisites:</b><br />
 
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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:
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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:<br />
 
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "biomolecules" -->
 
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*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 
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This unit builds on material covered in the following prerequisite units:
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This unit builds on material covered in the following prerequisite units:<br />
 
*You are expected to know the names, structures and (bio)chemical properties of the 20 proteinogenic amino acids;
 
*You are expected to know the names, structures and (bio)chemical properties of the 20 proteinogenic amino acids;
 
*[[BIN-Abstractions|BIN-Abstractions (Abstractions for Bioinformatics)]]
 
*[[BIN-Abstractions|BIN-Abstractions (Abstractions for Bioinformatics)]]
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Revision as of 12:39, 16 September 2020

Sequence

(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.

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[1] 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.

    • 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.

    This unit builds on material covered in the following prerequisite units:


     


    This page is tagged for revision; expect changes and proceed with caution.


     



     


    Contents

    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.
    • 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.


     


     


    Self-evaluation

    Notes

    1. ↑ Technically there are 21 proteinogenic amino acids, because some proteins contain Selenocysteine 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. One-letter code is U - as in PlUto.

    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


     



     

    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.


     

    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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