BIN-GENOME-Genome Annotation

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Genome annotation


 

Keywords:  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.


 


This unit ...

Prerequisites

You need to complete the following units before beginning this one:


 


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.


 


Evaluation

Evaluation: NA

This unit is not evaluated for course marks.


 


Contents

Task:



 


Further reading, links and resources


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

PubMed ] [ DOI ]

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

PubMed ] [ DOI ]

Tyner et al. (2017) The UCSC Genome Browser database: 2017 update. Nucleic Acids Res 45:D626-D634. (pmid: 27899642)

PubMed ] [ DOI ]

Aken et al. (2017) Ensembl 2017. Nucleic Acids Res 45:D635-D642. (pmid: 27899575)

PubMed ] [ DOI ]

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 ]

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

PubMed ] [ DOI ]



 


Notes


 


Self-evaluation

 



 




 

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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