Difference between revisions of "BIN-GENOME-Genome Annotation"
m |
m |
||
Line 28: | Line 28: | ||
== Abstract == | == Abstract == | ||
<section begin=abstract /> | <section begin=abstract /> | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "abstract" --> |
Introduction to genome annotation: the content of genomes - what to look for; identifying genes, and keeping up-to-date on methods. | Introduction to genome annotation: the content of genomes - what to look for; identifying genes, and keeping up-to-date on methods. | ||
<section end=abstract /> | <section end=abstract /> | ||
Line 37: | Line 37: | ||
== This unit ... == | == This unit ... == | ||
=== Prerequisites === | === Prerequisites === | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "prerequisites" --> |
− | <!-- included from "ABC-unit_components. | + | <!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" --> |
You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
*[[BIN-Genome-Sequencing|BIN-Genome-Sequencing (Genome sequencing)]] | *[[BIN-Genome-Sequencing|BIN-Genome-Sequencing (Genome sequencing)]] | ||
Line 46: | Line 46: | ||
=== Objectives === | === Objectives === | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "objectives" --> |
This unit will ... | This unit will ... | ||
* ... introduce categories of genome contents, as defined eg. through the ENCODE project, and discuss annotation methods. | * ... introduce categories of genome contents, as defined eg. through the ENCODE project, and discuss annotation methods. | ||
Line 54: | Line 54: | ||
=== Outcomes === | === Outcomes === | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "outcomes" --> |
After working through this unit you ... | After working through this unit you ... | ||
* ... are familar with the contents of genomes, some methods to annotate protein genes, and sources for genomes; | * ... are familar with the contents of genomes, some methods to annotate protein genes, and sources for genomes; | ||
Line 63: | Line 63: | ||
=== Deliverables === | === Deliverables === | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "deliverables" --> |
− | <!-- included from "ABC-unit_components. | + | <!-- 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. | ||
− | <!-- included from "ABC-unit_components. | + | <!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" --> |
*<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. | *<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. | ||
− | <!-- included from "ABC-unit_components. | + | <!-- 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]]. | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
{{Vspace}} | {{Vspace}} | ||
Line 86: | Line 77: | ||
<div id="BIO"> | <div id="BIO"> | ||
== Contents == | == Contents == | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "contents" --> |
{{Task|1= | {{Task|1= | ||
Line 131: | Line 122: | ||
== Notes == | == Notes == | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "notes" --> |
− | <!-- included from "ABC-unit_components. | + | <!-- included from "./data/ABC-unit_components.txt", section: "notes" --> |
<references /> | <references /> | ||
Line 141: | Line 132: | ||
<div id="ABC-unit-framework"> | <div id="ABC-unit-framework"> | ||
== Self-evaluation == | == Self-evaluation == | ||
− | <!-- included from " | + | <!-- included from "./components/BIN-Genome-Annotation.components.txt", section: "self-evaluation" --> |
<!-- | <!-- | ||
=== Question 1=== | === Question 1=== | ||
Line 166: | Line 157: | ||
− | <!-- included from "ABC-unit_components. | + | <!-- included from "./data/ABC-unit_components.txt", section: "ABC-unit_ask" --> |
---- | ---- | ||
Line 194: | Line 185: | ||
</div> | </div> | ||
[[Category:ABC-units]] | [[Category:ABC-units]] | ||
− | <!-- included from "ABC-unit_components. | + | <!-- included from "./data/ABC-unit_components.txt", section: "ABC-unit_footer" --> |
{{CC-BY}} | {{CC-BY}} |
Revision as of 01:24, 6 January 2018
Genome annotation
Keywords: Genome contents; ENCODE; Genome annotation methods.
Contents
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.
Contents
Task:
- Read the introductory notes on the annotation of genome sequences.
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)
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
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.