Difference between revisions of "BIN-GENOME-Genome Annotation"

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Genome annotation
 
Genome annotation
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(Genome contents; ENCODE; Genome annotation methods.)
 
(Genome contents; ENCODE; Genome annotation methods.)
 
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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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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 />
 
*[[BIN-Genome-Sequencing|BIN-Genome-Sequencing (Genome sequencing)]]
 
*[[BIN-Genome-Sequencing|BIN-Genome-Sequencing (Genome sequencing)]]
 
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Revision as of 12:38, 16 September 2020

Genome annotation

(Genome contents; ENCODE; Genome annotation methods.)


 


Abstract:

Introduction to genome annotation: the content of genomes - what to look for; identifying genes, and keeping up-to-date on methods.


Objectives:
This unit will ...

  • ... introduce categories of genome contents, as defined eg. through the ENCODE project, and discuss annotation methods.

Outcomes:
After working through this unit you ...

  • ... are familar with the contents of genomes, some methods to annotate protein genes, and sources for genomes;
  • ... know how to get up-to-date information on genome annotation workflows.

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:
    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:


    Self-evaluation

    Notes

    Further reading, links and resources

    Encode
    Davis et al. (2018) The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res 46:D794-D801. (pmid: 29126249)

    PubMed ] [ DOI ]

    ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9:e1001046. (pmid: 21526222)

    PubMed ] [ DOI ]


     

    Annotation example papers
    Lok et al. (2017) De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis). G3 (Bethesda) 7:755-773. (pmid: 28087693)

    PubMed ] [ DOI ]

    Seo et al. (2016) De novo assembly and phasing of a Korean human genome. Nature 538:243-247. (pmid: 27706134)

    PubMed ] [ DOI ]

    Amemiya et al. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature 496:311-6. (pmid: 23598338)

    PubMed ] [ DOI ]



    Specific topics
    Copy Number Variation
    Zarrei et al. (2015) A copy number variation map of the human genome. Nat Rev Genet 16:172-83. (pmid: 25645873)

    PubMed ] [ DOI ]

     
    miRNA
    Bracken et al. (2016) A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet 17:719-732. (pmid: 27795564)

    PubMed ] [ DOI ]

     
    Epigenomics
    Stricker et al. (2017) From profiles to function in epigenomics. Nat Rev Genet 18:51-66. (pmid: 27867193)

    PubMed ] [ DOI ]


     




     

    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:

    2017-08-05

    Version:

    1.0

    Version history:

    • 1.0 First live version
    • 0.1 First stub

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