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Keywords: Genome contents; ENCODE; Genome annotation methods | |||||||
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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. |
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Evaluation: NA: This unit is not evaluated for course marks. |
Introduction to genome annotation: the content of genomes - what to look for; identifying genes, and keeping up-to-date on methods.
Task…
Aziz, Ramy
K et al.. (2008). “The RAST Server: rapid annotations
using subsystems technology”. Bmc Genomics
9:75 .
[PMID: 18261238]
[DOI: 10.1186/1471-2164-9-75]
Salzberg, Steven
L. (2019). “Next-generation genome annotation: we still struggle
to get it right”. Genome Biology 20(1):92
.
[PMID: 31097009]
[DOI: 10.1186/s13059-019-1715-2]
Ejigu, Girum
F and Jaehee Jung. (2020). “Review on the Computational Genome
Annotation of Sequences Obtained by Next-Generation Sequencing”.
Biology 9(9):.
[PMID: 32962098]
[DOI: 10.3390/biology9090295]
Encode The ENCODE project
Davis, Carrie
A et al.. (2018). “The Encyclopedia of DNA elements
(ENCODE): data portal update”. Nucleic Acids Research
46(D1):D794–D801 .
[PMID:
29126249]
[DOI: 10.1093/nar/gkx1081]
ENCODE Project
Consortium. (2011). “A user’s guide to the encyclopedia of DNA
elements (ENCODE)”. Plos Biology 9(4):e1001046
.
[PMID: 21526222]
[DOI: 10.1371/journal.pbio.1001046]
Annotation example papers
Lok, Si
et al.. (2017). “De Novo Genome and Transcriptome Assembly of the
Canadian Beaver (Castor canadensis)”. G3 (Bethesda, Md.)
7(2):755–773 .
[PMID: 28087693]
[DOI: 10.1534/g3.116.038208]
Seo,
Jeong-Sun et al.. (2016). “De novo assembly and phasing of
a Korean human genome”. Nature
538(7624):243–247 .
[PMID: 27706134]
[DOI: 10.1038/nature20098]
Amemiya, Chris
T et al.. (2013). “The African coelacanth genome provides
insights into tetrapod evolution”. Nature
496(7445):311–6 .
[PMID:
23598338]
[DOI: 10.1038/nature12027]
Zarrei,
Mehdi et al.. (2015). “A copy number variation map of the
human genome”. Nature Reviews. Genetics
16(3):172–83 .
[PMID: 25645873]
[DOI: 10.1038/nrg3871]
Bracken, Cameron
P, Hamish S Scott, and Gregory J Goodall. (2016). “A
network-biology perspective of microRNA function and dysfunction in
cancer”. Nature Reviews. Genetics
17(12):719–732 .
[PMID:
27795564]
[DOI: 10.1038/nrg.2016.134]
Stricker, Stefan
H, Anna Köferle, and Stephan Beck. (2017). “From profiles to
function in epigenomics”. Nature Reviews. Genetics
18(1):51–66 .
[PMID: 27867193]
[DOI: 10.1038/nrg.2016.138]
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