Difference between revisions of "BIN-SEQA-Composition"

From "A B C"
Jump to navigation Jump to search
m
m
Line 1: Line 1:
−
<div id="BIO">
+
<div id="ABC">
−
  <div class="b1">
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Analysis of Sequence Composition
 
Analysis of Sequence Composition
−
  </div>
+
<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
−
 
+
(Analysis of sequence composition.)
−
  {{Vspace}}
+
</div>
−
 
 
−
<div class="keywords">
 
−
<b>Keywords:</b>&nbsp;
 
−
Analysis of sequence composition.
 
 
</div>
 
</div>
  
−
{{Vspace}}
+
{{Smallvspace}}
−
 
 
−
 
 
−
__TOC__
 
−
 
 
−
{{Vspace}}
 
  
  
−
{{LIVE}}
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
−
 
+
<div style="font-size:118%;">
−
{{Vspace}}
+
<b>Abstract:</b><br />
−
 
 
−
 
 
−
</div>
 
−
<div id="ABC-unit-framework">
 
−
== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
−
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "abstract" -->
 
 
The most basic step of sequence analysis is to ask: what amino acids does a sequence contain.
 
The most basic step of sequence analysis is to ask: what amino acids does a sequence contain.
 
<section end=abstract />
 
<section end=abstract />
−
 
+
</div>
−
{{Vspace}}
+
<!-- ============================ -->
−
 
+
<hr>
−
 
+
<table>
−
== This unit ... ==
+
<tr>
−
=== Prerequisites ===
+
<td style="padding:10px;">
−
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "prerequisites" -->
+
<b>Objectives:</b><br />
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes-external_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:
 
−
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "biomolecules" -->
 
−
*<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.
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 
−
You need to complete the following units before beginning this one:
 
−
*[[BIN-SEQA-Concepts|BIN-SEQA-Concepts (Concepts of Sequence Analysis)]]
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
=== Objectives ===
 
−
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* ... introduce basic compositional amino acid analysis;
 
* ... introduce basic compositional amino acid analysis;
 
* ... teach how to prodcue barplots of enrichment ratios;
 
* ... teach how to prodcue barplots of enrichment ratios;
−
 
+
</td>
−
{{Vspace}}
+
<td style="padding:10px;">
−
 
+
<b>Outcomes:</b><br />
−
 
 
−
=== Outcomes ===
 
−
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "outcomes" -->
 
 
After working through this unit you ...
 
After working through this unit you ...
 
* ... are familar with comparing observed to reference frequencies;
 
* ... are familar with comparing observed to reference frequencies;
 
* ... can use tools from the seqinr package for simple amino acid analysis;
 
* ... can use tools from the seqinr package for simple amino acid analysis;
 
* ... can produce barplots of log(ratio) data.
 
* ... can produce barplots of log(ratio) data.
−
 
+
</td>
−
{{Vspace}}
+
</tr>
−
 
+
</table>
−
 
+
<!-- ============================ -->
−
=== Deliverables ===
+
<hr>
−
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "deliverables" -->
+
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
*<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.
 
*<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.
Line 76: Line 46:
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
<!-- included from "./data/ABC-unit_components.txt", section: "notes-external_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:
 +
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "biomolecules" -->
 +
*<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.
 +
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 +
This unit builds on material covered in the following prerequisite units:
 +
*[[BIN-SEQA-Concepts|BIN-SEQA-Concepts (Concepts of Sequence Analysis)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
 +
 +
{{Smallvspace}}
 +
 +
 +
 +
{{Smallvspace}}
 +
 +
 +
__TOC__
  
 
{{Vspace}}
 
{{Vspace}}
  
  
−
</div>
 
−
<div id="BIO">
 
 
== Contents ==
 
== Contents ==
 
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "contents" -->
 
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "contents" -->
Line 119: Line 111:
 
{{Vspace}}
 
{{Vspace}}
  
−
 
−
{{Vspace}}
 
−
 
−
 
−
== Further reading, links and resources ==
 
−
<!-- {{#pmid: 19957275}} -->
 
−
<!-- {{WWW|WWW_GMOD}} -->
 
−
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
−
 
−
{{Vspace}}
 
−
 
−
 
−
== Notes ==
 
−
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "notes" -->
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 
−
<references />
 
−
 
−
{{Vspace}}
 
−
 
−
 
−
</div>
 
−
<div id="ABC-unit-framework">
 
 
== Self-evaluation ==
 
== Self-evaluation ==
−
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "self-evaluation" -->
 
 
<!--
 
<!--
 
=== Question 1===
 
=== Question 1===
Line 159: Line 128:
  
 
-->
 
-->
−
 
+
== Notes ==
−
{{Vspace}}
+
<!-- included from "./components/BIN-SEQA-Composition.components.txt", section: "notes" -->
−
 
+
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
−
 
+
<references />
 +
== Further reading, links and resources ==
 +
<!-- {{#pmid: 19957275}} -->
 +
<!-- {{WWW|WWW_GMOD}} -->
 +
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
  
 
{{Vspace}}
 
{{Vspace}}

Revision as of 19:32, 26 January 2018

Analysis of Sequence Composition

(Analysis of sequence composition.)


 


Abstract:

The most basic step of sequence analysis is to ask: what amino acids does a sequence contain.

Objectives:
This unit will ...

  • ... introduce basic compositional amino acid analysis;
  • ... teach how to prodcue barplots of enrichment ratios;

Outcomes:
After working through this unit you ...

  • ... are familar with comparing observed to reference frequencies;
  • ... can use tools from the seqinr package for simple amino acid analysis;
  • ... can produce barplots of log(ratio) data.

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:


 



 



 


Contents

Task:


EMBOSS Tools

 

Task:

Local composition
  1. Find pepinfo under the PROTEIN COMPOSITION heading.
  2. Retrieve the MYSPE Mbp1 related sequence from your R database, e.g. with something like
    cat(db$protein[db$protein$name == "UMAG_1122"), "sequence"]
  3. Copy and paste the sequence into the input field.
  4. Run with default parameters.
  5. Scroll to the figures all the way at the bottom.
  6. Do the same in a separate window for yeast Mbp1.
  7. Try to compare ... (kind of hard without reference, overlay and expectation, isn't it?)
 
Global composition
  1. Find pepstats under the PROTEIN COMPOSITION heading.
  2. Paste the MYSPE Mbp1 sequence into the input field.
  3. Run with default parameters.
  4. Do the same in a separate window for yeast Mbp1.
  5. Try to compare ... are there significant and unexpected differences?


 

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-SEQA-Composition.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

Further reading, links and resources

 



 

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:

2017-11-14

Version:

1.0

Version history:

  • 1.0 First live
  • 0.1 First stub

CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-SEQA-Composition&oldid=10823"