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

From "A B C"
Jump to navigation Jump to search
m
m
Line 1: Line 1:
 
<div id="ABC">
 
<div id="ABC">
<div style="padding:5px; border:1px solid #000000; background-color:#f4d7b7; font-size:300%; font-weight:400; color: #000000; width:100%;">
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Genome annotation
 
Genome annotation
<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#f4d7b7; font-size:30%; font-weight:200; color: #000000; ">
+
<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
 
(Genome contents; ENCODE; Genome annotation methods.)
 
(Genome contents; ENCODE; Genome annotation methods.)
 
</div>
 
</div>
Line 10: Line 10:
  
  
<div style="padding:5px; border:1px solid #000000; background-color:#f4d7b733; font-size:85%;">
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
 
<div style="font-size:118%;">
 
<div style="font-size:118%;">
 
<b>Abstract:</b><br />
 
<b>Abstract:</b><br />
Line 55: Line 55:
  
  
{{REVISE}}
 
  
 
{{Smallvspace}}
 
{{Smallvspace}}
Line 72: Line 71:
 
{{Task|1=
 
{{Task|1=
 
*Read the introductory notes on {{ABC-PDF|BIN-Genome-Annotation|the annotation of genome sequences}}.
 
*Read the introductory notes on {{ABC-PDF|BIN-Genome-Annotation|the annotation of genome sequences}}.
 +
* Visit the [https://rast.nmpdr.org/ '';'' server Website] - (more publications linked from there). For many currently published genome-sequencing projects this is the standard of annotation.
 +
{{#pmid:18261238}}
 +
 
}}
 
}}
  
  
== Self-evaluation ==
+
== Further reading, links and resources ==
<!--
 
=== Question 1===
 
  
Question ...
+
;General:
 +
{{#pmid: 31097009}}
 +
{{#pmid: 32962098}}
  
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
+
{{Smallvspace}}
Answer ...
 
<div class="mw-collapsible-content">
 
Answer ...
 
  
</div>
+
----
  </div>
 
 
 
  {{Vspace}}
 
 
 
-->
 
== Further reading, links and resources ==
 
  
 
;Encode:
 
;Encode:
Line 99: Line 92:
 
{{#pmid: 21526222}}
 
{{#pmid: 21526222}}
  
{{Vspace}}
+
{{Smallvspace}}
  
 
----
 
----
Line 135: Line 128:
 
:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
:2017-08-05
+
:2020-09-25
 
<b>Version:</b><br />
 
<b>Version:</b><br />
:1.0
+
:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.1 2020 Updates
 
*1.0 First live version
 
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
Line 147: Line 141:
 
[[Category:ABC-units]]
 
[[Category:ABC-units]]
 
{{UNIT}}
 
{{UNIT}}
{{REVISE}}
+
{{LIVE}}
 
</div>
 
</div>
 
<!-- [END] -->
 
<!-- [END] -->

Revision as of 05:19, 26 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:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:

    Aziz et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. (pmid: 18261238)

    PubMed ] [ DOI ]


    Further reading, links and resources

    General
    Salzberg (2019) Next-generation genome annotation: we still struggle to get it right. Genome Biol 20:92. (pmid: 31097009)

    PubMed ] [ DOI ]

    Ejigu & Jung (2020) Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. Biology (Basel) 9:. (pmid: 32962098)

    PubMed ] [ DOI ]


     

    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 ]

    Notes


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-25

    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.