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THANK YOU

 

Remove all the instructions and examples in italic (including this yellow header) and replace by your text as needed but please do not italicize your text, as italic is hard to read.

 

 

Your Title Here (team name - tool[s] or specific approach)
e.g. “University of Maryland – SuperVis”

VAST 2010 Challenge
Genetic Sequences – Tracing the Mutations of a Disease

Authors and Affiliations:

e.g. Tom Jones, University of Maryland, Jones@cs.umd.edu  [PRIMARY contact]
       Mary Smith, University of Massachusetts, Lowell, [email]
      Paul White, University of Maryland [Faculty advisor], [email]
      (NOTE: the PRIMARY contact needs to be joinable by email for a week after submission and again before the Sept. 1st deadline for camera ready materials)

Tool(s):

Provide a short description of the tool(s) you used. Mention where and when it was developed.
Additional credit to developers of the tools can be provided here, and links to find more information on the tool. 

If the tool used is a toolkit, rate the effort needed to customize the toolkit for this specific analysis. Consider such things as programming ability required, amount of time needed.

(250 words MAX)

 

Video:

 

Replace this line by a link to your video.

 

 

ANSWERS:

MC3.1: What is the region or country of origin for the current outbreak?  Please provide your answer as the name of the native viral strain along with a brief explanation.

Replace this line with your Short Answer.  Please see the definition of a short answer in the Task Descriptions.

MC3.2:  Over time, the virus spreads and the diversity of the virus increases as it mutates.  Two patients infected with the Drafa virus are in the same hospital as Nicolai.  Nicolai has a strain identified by sequence 583.  One patient has a strain identified by sequence 123 and the other has a strain identified by sequence 51.  Assume only a single viral strain is in each patient.  Which patient likely contracted the illness from Nicolai and why?  Please provide your answer as the sequence number along with a brief explanation.

Replace this line with your Short Answer.  Please see the definition of a short answer in the Task Descriptions.

MC3.3:  Signs and symptoms of the Drafa virus are varied and humans react differently to infection.  Some mutant strains from the current outbreak have been reported as being worse than others for the patients that come in contact with them. 

Identify the top 3 mutations that lead to an increase in symptom severity (a disease characteristic).  The mutations involve one or more base substitutions.  For this question, the biological properties of the underlying amino acid sequence patterns are not significant in determining disease characteristics.

For each mutation provide the base substitutions and their position in the sequence (left to right) where the base substitutions occurred. For example,

C → G, 456 (C changed to G at position 456)

G → A, 513 and T → A, 907 (G changed to A at position 513 and T changed to A at position 907)

A → G, 39 (A changed to G at position 39)

Replace this line with your Short Answer.  Please see the definition of a short answer in the Task Descriptions.

MC3.4:  Due to the rapid spread of the virus and limited resources, medical personnel would like to focus on treatments and quarantine procedures for the worst of the mutant strains from the current outbreak, not just symptoms as in the previous question.  To find the most dangerous viral mutants, experts are monitoring multiple disease characteristics.

Consider each virulence and drug resistance characteristic as equally important.  Identify the top 3 mutations that lead to the most dangerous viral strains. The mutations involve one or more base substitutions.  In a worst case scenario, a very dangerous strain could cause severe symptoms, have high mortality, cause major complications, exhibit resistance to anti viral drugs, and target high risk groups.  For this question, the biological properties of the underlying amino acid sequence patterns are not significant in determining disease characteristics.

For each mutation provide the base substitutions and their position in the sequence (left to right) where the base substitutions occurred. For example,

C → G, 456 (C changed to G at position 456)

G → A, 513 and T → A, 907 (G changed to A at position 513 and T changed to A at position 907)

A → G, 39 (A changed to G at position 39).

Replace this line with your Detailed Answer.  Please see the definition of a detailed answer in the Task Descriptions.