Difference between revisions of "BIN-Sequence"

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<div id="BIO">
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<div id="ABC">
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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%;">
 
Sequence
 
Sequence
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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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(The 20 amino acids and the one-letter code)
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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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The 20 amino acids and the one-letter code
 
 
</div>
 
</div>
  
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{{Smallvspace}}
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__TOC__
 
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{{DEV}}
 
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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<section begin=abstract />
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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.
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<section end=abstract />
 
</div>
 
</div>
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<div id="ABC-unit-framework">
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<!-- ============================  -->
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== Abstract ==
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<hr>
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "abstract" -->
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<table>
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...
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<tr>
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<td style="padding:10px;">
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{{Vspace}}
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<b>Objectives:</b><br />
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This unit will ...
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* 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;
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== This unit ... ==
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* list the conventions we use when writing sequence;
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=== Prerequisites ===
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* 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;
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "prerequisites" -->
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* demonstrate R code to read, analyse and manipulate strings.
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<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
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</td>
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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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<td style="padding:10px;">
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<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
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<b>Outcomes:</b><br />
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After working through this unit you ...
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* can draw the structure formula of all 20 proteinogenic amino acids<ref>''Technically'' there are 21 proteinogenic amino acids, because some proteins contain {{WP|Selenocysteine}} translated from TGA codons. However this is not universal, and thus '''<tt>Sec</tt>''' is as much a proteinogenic amino acid as [https://www.jpl.nasa.gov/spaceimages/images/wallpaper/PIA20291-800x600.jpg Pluto is not a planet]. Technically correct. The memnonic for the <tt>Sec</tt> one-letter code '''U''' is: u as in Pl'''U'''to.</ref> 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";
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* can competently read, analyse and manipulate strings in R;
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* can shuffle sequences (permute them) and create sequences with specific target ditributions of characters, in R.
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</td>
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</tr>
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</table>
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<!-- ============================ -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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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>
 +
<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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<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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<section end=deliverables />
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<!-- ============================  -->
 +
<hr>
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<section begin=prerequisites />
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<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.
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<!-- 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 />
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You need to complete the following units before beginning this one:
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*You are expected to know the names, structures and (bio)chemical properties of the 20 proteinogenic amino acids;
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*[[BIN-Abstractions]]
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*[[BIN-Abstractions|BIN-Abstractions (Abstractions for Bioinformatics)]]
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*[[FND-Genetic_code]]
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*[[FND-Genetic_code|FND-Genetic_code (Genetic Code)]]
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<section end=prerequisites />
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<!-- ============================  -->
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</div>
  
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{{Smallvspace}}
  
  
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=== Objectives ===
 
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "objectives" -->
 
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...
 
  
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{{Smallvspace}}
  
  
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=== Outcomes ===
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__TOC__
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "outcomes" -->
 
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...
 
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=== Deliverables ===
 
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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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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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|course journal]].
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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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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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "evaluation" -->
 
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<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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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "contents" -->
 
 
{{Task|1=
 
{{Task|1=
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*Read the introductory notes on {{ABC-PDF|BIN-Sequence|the idea of biomolecular "sequence"}}.
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*Read the introductory notes on {{ABC-PDF|BIN-Sequence|the concept of biomolecular "sequence"}}.
 
}}
 
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{{ABC-unit|BIN-Sequence.R}}
  
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{{Smallvspace}}
  
  
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== Self-evaluation ==
  
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* Answer the [[Amino_Acid_Exam_Questions| questions on amino acids from '''2002 - 2009 BCH441 Final Exam''' questions]].
  
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== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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<!-- included from "../components/BIN-Sequence.components.wtxt", section: "notes" -->
 
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<references />
 
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== Self-evaluation ==
 
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<!--
 
<!--
 
=== Question 1===
 
=== Question 1===
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-->
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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://en.wikipedia.org/wiki/Amino_acid '''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.</div>
 +
<div class="reference-box">[https://en.wikipedia.org/wiki/Sense_(molecular_biology) '''The "sense" of how nucleotide sequences are written''' (Wikipedia)]</div>
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<div class="reference-box">[https://github.com/tidyverse/stringr Introduction to the <tt>'''stringr'''</tt> package]</div>
  
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== Notes ==
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<references />
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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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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-08-05
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:2020-09-23
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.1 2020 Updates
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*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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[[Category:ABC-units]]
 
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{{CC-BY}}
 
{{CC-BY}}
  
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[[Category:ABC-units]]
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Latest revision as of 13:22, 23 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 competently 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:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    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

    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

    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. The memnonic for the Sec one-letter code U is: u as in PlUto.


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-23

    Version:

    1.1

    Version history:

    • 1.1 2020 Updates
    • 1.0 First live version
    • 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-Sequence&oldid=11623"