Difference between revisions of "BIN-SEQA-Composition"

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<div id="BIO">
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<div id="ABC">
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  <div class="b1">
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
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Analysis of Sequence Constitution
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Analysis of Sequence Composition
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Analysis of sequence composition.)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Analysis of sequence constitution (with R examples)
 
 
</div>
 
</div>
  
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{{Vspace}}
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{{Smallvspace}}
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__TOC__
 
  
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{{Vspace}}
 
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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{{DEV}}
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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{{Vspace}}
 
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</div>
 
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", 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 />
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</div>
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{{Vspace}}
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<!-- ============================  -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
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This unit will ...
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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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* ... introduce basic compositional amino acid analysis;
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<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
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* ... teach how to prodcue barplots of enrichment ratios;
 +
</td>
 +
<td style="padding:10px;">
 +
<b>Outcomes:</b><br />
 +
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.
 +
</td>
 +
</tr>
 +
</table>
 +
<!-- ============================ -->
 +
<hr>
 +
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 +
<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>
 +
<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>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
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 />
 
*<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.
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
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This unit builds on material covered in the following prerequisite units:<br />
−
You need to complete the following units before beginning this one:
 
 
*[[BIN-SEQA-Concepts|BIN-SEQA-Concepts (Concepts of Sequence Analysis)]]
 
*[[BIN-SEQA-Concepts|BIN-SEQA-Concepts (Concepts of Sequence Analysis)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
  
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{{Vspace}}
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{{Smallvspace}}
  
  
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=== Objectives ===
 
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "objectives" -->
 
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This unit will ...
 
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* ... introduce ;
 
−
* ... demonstrate ;
 
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* ... teach ;
 
  
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{{Vspace}}
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{{Smallvspace}}
  
  
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=== Outcomes ===
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__TOC__
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "outcomes" -->
 
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After working through this unit you ...
 
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* ... can ;
 
−
* ... are familar with ;
 
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* ... have begun to.
 
−
 
 
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{{Vspace}}
 
−
 
 
−
 
 
−
=== Deliverables ===
 
−
<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "deliverables" -->
 
−
<!-- included from "ABC-unit_components.wtxt", 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.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
−
*<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.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
  
 
{{Vspace}}
 
{{Vspace}}
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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "evaluation" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
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:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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{{Vspace}}
 
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</div>
 
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "contents" -->
 
 
{{Task|1=
 
{{Task|1=
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*Read the introductory notes on {{ABC-PDF|BIN-SEQA-Constitution|"Constitution" as a paradigm for sequence analysis}}.
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*Read the introductory notes on {{ABC-PDF|BIN-SEQA-Composition|"Composition" as a paradigm for sequence analysis}}.
 
}}
 
}}
  
  
 +
===EMBOSS Tools ===
 +
{{Smallvspace}}
 
{{task|1=
 
{{task|1=
 +
 +
*Navigate to an instance of the "EMBOSS explorer" e.g. at [http://www.bioinformatics.nl/emboss-explorer/ '''bioinformatics.nl''']
 +
 
;Local composition
 
;Local composition
 
# Find <code>pepinfo</code> under the '''PROTEIN COMPOSITION''' heading.
 
# Find <code>pepinfo</code> under the '''PROTEIN COMPOSITION''' heading.
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# Retrieve the MYSPE Mbp1 related sequence from your '''R''' database, e.g. with something like <br /><code>  cat(db$protein[db$protein$name == "UMAG_1122"), "sequence"]</code>
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# Retrieve the MYSPE Mbp1 related sequence from your '''R''' database, e.g. with something like <br /><code>  cat(myDB$protein[myDB$protein$name == "PHD1_SACCE" , "sequence"])</code>
 
# Copy and paste the sequence into the input field.
 
# Copy and paste the sequence into the input field.
 
# Run with default parameters.
 
# Run with default parameters.
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# Scroll to the figures all the way at the bottom.
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# Scroll to the figures <ul>all the way at the bottom</ul>.
 
# Do the same in a separate window for yeast Mbp1.
 
# Do the same in a separate window for yeast Mbp1.
 
# Try to compare ... <small>(kind of hard without reference, overlay and expectation, isn't it?)</small>
 
# Try to compare ... <small>(kind of hard without reference, overlay and expectation, isn't it?)</small>
−
}}
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{{Vspace}}
  
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{{task|1=
 
 
;Global composition
 
;Global composition
 
# Find <code>pepstats</code> under the '''PROTEIN COMPOSITION''' heading.
 
# Find <code>pepstats</code> under the '''PROTEIN COMPOSITION''' heading.
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# Try to compare ... are there significant and unexpected differences?
 
# Try to compare ... are there significant and unexpected differences?
 
}}
 
}}
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{{Vspace}}
 
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{{Vspace}}
 
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== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- {{WWW|WWW_GMOD}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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{{Vspace}}
 
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== Notes ==
 
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "notes" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
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<references />
 
  
 
{{Vspace}}
 
{{Vspace}}
  
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{{ABC-unit|BIN-SEQA-Composition.R}}
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</div>
 
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<div id="ABC-unit-framework">
 
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== Self-evaluation ==
 
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<!-- included from "../components/BIN-SEQA-Constitution.components.wtxt", section: "self-evaluation" -->
 
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<!--
 
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=== Question 1===
 
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Question ...
 
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<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
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Answer ...
 
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<div class="mw-collapsible-content">
 
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Answer ...
 
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</div>
 
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  </div>
 
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  {{Vspace}}
 
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-->
 
  
 
{{Vspace}}
 
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<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_ask" -->
 
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----
 
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{{Vspace}}
 
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<b>If in doubt, ask!</b> 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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----
 
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{{Vspace}}
 
  
 
<div class="about">
 
<div class="about">
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-11-14
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:2020-09-24
 
<b>Version:</b><br />
 
<b>Version:</b><br />
−
:1.0
+
:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.1 2020 Maintenance
 
*1.0 First live
 
*1.0 First live
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
</div>
−
[[Category:ABC-units]]
 
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<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_footer" -->
 
  
 
{{CC-BY}}
 
{{CC-BY}}
  
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[[Category:ABC-units]]
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{{UNIT}}
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{{LIVE}}
 
</div>
 
</div>
 
<!-- [END] -->
 
<!-- [END] -->

Latest revision as of 15:51, 24 September 2020

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:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    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(myDB$protein[myDB$protein$name == "PHD1_SACCE" , "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.


     


     


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-24

    Version:

    1.1

    Version history:

    • 1.1 2020 Maintenance
    • 1.0 First live
    • 0.1 First stub

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