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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− | + | <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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− | + | <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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− | This unit builds on material covered in the following prerequisite units: | + | 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:
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Outcomes:
|
Deliverables:
Prerequisites:
This unit builds on material covered in the following prerequisite units:
Contents
Task:
- Read the introductory notes on the annotation of genome sequences.
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) |
ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9:e1001046. (pmid: 21526222) |
- 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) |
Seo et al. (2016) De novo assembly and phasing of a Korean human genome. Nature 538:243-247. (pmid: 27706134) |
Amemiya et al. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature 496:311-6. (pmid: 23598338) |
- 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) - miRNA
Bracken et al. (2016) A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet 17:719-732. (pmid: 27795564) - Epigenomics
Stricker et al. (2017) From profiles to function in epigenomics. Nat Rev Genet 18:51-66. (pmid: 27867193)
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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