ABC-INT-Genome annotation

Integration Unit: Genome annotation

 

Keywords:  Integrator unit: annotate sequences in a genome

 

 

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This page is only a stub; it is here as a placeholder to establish the logical framework of the site but there is no significant content as yet. Do not work with this material until it is updated to "live" status.

 

Abstract

This page assesses the learning units for data management and sequence analysis of genomic sequence data.

• choose a fungal genome
• create a datamodel for domain annotations
• implement as a dataframe
• annotate signal sequence (or disordered stretches)
• plot and analyze results

 

This unit ...

Prerequisites

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

• BIN-FUNC-Annotation (Function Annotation)
• BIN-Genome-Browsers (Genome Browsers)

 

Objectives

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Outcomes

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Deliverables

• No separate deliverables: This unit collects other units and has no deliverables on its own.

 

Evaluation

This "Integrator Unit" should be submitted for evaluation for a maximum of 8 marks if one of the written deliverables is chosen, resp. 16 marks for the oral exam.

Please note the evaluation types that are available as options for this unit. Choose one evaluation type that you have not chosen for another Integrator Unit. (Each submitted Integrator Unit must be evaluated in a different way and one of your evaluations - but not your first one - must be an oral exam).

 

Interview option

Identify a laboratory whose work includes genome annotation, or re-annotation. Get in touch with the PI, a postdoc or senior graduate student in the laboratory and interview them in person or by eMail. Find out

• why this work is important;
• how they approach it methodologically;
• in particular, what features they are looking for, and what discoveries can be made by looking for these features (get very specific on that point, we are most interested in strategies for interpretation of data);
• what they have recently learned;
• what the major challenges, current discussions, or controversies are.
• write up your interview on a subpage of your User page of the Student Wiki;
• add information that may be required to understand the methodology;
• make sure that you have included important literature references.
• When you are done with everything, add the following category tag to the page:

[[Category:EVAL-INT-Genome_annotation]]

Do not change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.

 

 

Contents

This is a "milestone unit". Its purpose is merely to collect a number of preparatory units into a single, common prerequisite. It has no contents of its own; you are expected to be familiar and competent with all preparatory material at this point.

 

Further reading, links and resources

 

Notes

 

Self-evaluation

 

 

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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.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-08-09

Version:

0.1

Version history:

• 0.1 First stub

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