Difference between revisions of "BIN-SEQA-Concepts"

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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%;">
 
Concepts of Sequence Analysis
 
Concepts of Sequence Analysis
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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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(constitution cooncatenation comparison correspondence conservation composition collaboration; Web-services; analysis tools; bioinformatics.ca)
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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constitution cooncatenation comparison correspondence conservation composition collaboration; Web-services; analysis tools; bioinformatics.ca
 
 
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__TOC__
 
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{{LIVE}}
 
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<div id="ABC-unit-framework">
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<div style="font-size:118%;">
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== Abstract ==
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<b>Abstract:</b><br />
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "abstract" -->
 
 
This unit introduces a typology of sequence analysis strategies and presents common access points to sequence analysis tools.
 
This unit introduces a typology of sequence analysis strategies and presents common access points to sequence analysis tools.
 
<section end=abstract />
 
<section end=abstract />
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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-Concepts.components.txt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "./data/ABC-unit_components.txt", section: "notes-external_prerequisites" -->
 
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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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<!-- 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.
 
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<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[RPR-Biostrings|RPR-Biostrings (The biostrings R Package)]]
 
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*[[RPR-RegEx|RPR-RegEx (Regular Expressions (regex) with R)]]
 
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{{Vspace}}
 
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=== Objectives ===
 
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* ... introduce a typology of sequence analysis strategies;
 
* ... introduce a typology of sequence analysis strategies;
 
* ... discuss sound principles for developin sequence analysis experiments;
 
* ... discuss sound principles for developin sequence analysis experiments;
 
* ... showcase some access points to sequence analysis tools in common use.
 
* ... showcase some access points to sequence analysis tools in common use.
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</td>
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{{Vspace}}
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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=== Outcomes ===
 
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "outcomes" -->
 
 
After working through this unit you ...
 
After working through this unit you ...
 
* ... are familar with how sequence analysis strategies can be organized;
 
* ... are familar with how sequence analysis strategies can be organized;
 
* ... can critically evaluate your own sequence analysis experiments for completeness, soundness, and whether they can be extended;
 
* ... can critically evaluate your own sequence analysis experiments for completeness, soundness, and whether they can be extended;
 
* ... are familar with common access points to bioinformatics tools.
 
* ... are familar with common access points to bioinformatics tools.
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</table>
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<!-- ============================ -->
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=== Deliverables ===
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<hr>
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "deliverables" -->
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<b>Deliverables:</b><br />
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<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.
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<!-- 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]].
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<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:
 +
*[[RPR-Biostrings|RPR-Biostrings (The biostrings R Package)]]
 +
*[[RPR-RegEx|RPR-RegEx (Regular Expressions (regex) with R)]]
 +
<section end=prerequisites />
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<!-- ============================  -->
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</div>
  
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<div id="BIO">
 
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== Contents ==
 
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "contents" -->
 
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{{Task|1=
 
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*Read the introductory notes on {{ABC-PDF|BIN-SEQA-Concepts|categorizing the approaches to biological sequence analysis}}.
 
  
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}}
 
  
  
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__TOC__
  
 
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== Further reading, links and resources ==
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== Contents ==
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<!-- {{#pmid: 19957275}} -->
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "contents" -->
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<!-- {{WWW|WWW_GMOD}} -->
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{{Task|1=
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
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*Read the introductory notes on {{ABC-PDF|BIN-SEQA-Concepts|categorizing the approaches to biological sequence analysis}}.
  
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{{Vspace}}
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}}
  
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== Notes ==
 
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "notes" -->
 
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<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 
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<references />
 
  
 
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</div>
 
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<div id="ABC-unit-framework">
 
 
== Self-evaluation ==
 
== Self-evaluation ==
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<!-- included from "./components/BIN-SEQA-Concepts.components.txt", section: "self-evaluation" -->
 
 
<!--
 
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=== Question 1===
 
=== Question 1===
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== Notes ==
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<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
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<references />
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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> -->
  
 
{{Vspace}}
 
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Revision as of 19:32, 26 January 2018

Concepts of Sequence Analysis

(constitution cooncatenation comparison correspondence conservation composition collaboration; Web-services; analysis tools; bioinformatics.ca)


 


Abstract:

This unit introduces a typology of sequence analysis strategies and presents common access points to sequence analysis tools.

Objectives:
This unit will ...

  • ... introduce a typology of sequence analysis strategies;
  • ... discuss sound principles for developin sequence analysis experiments;
  • ... showcase some access points to sequence analysis tools in common use.

Outcomes:
After working through this unit you ...

  • ... are familar with how sequence analysis strategies can be organized;
  • ... can critically evaluate your own sequence analysis experiments for completeness, soundness, and whether they can be extended;
  • ... are familar with common access points to bioinformatics tools.

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:


 


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:

2017-11-09

Version:

1.0

Version history:

  • 1.0 First live
  • 0.1 First stub

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