Unit 1-Lecture 2

Question 1

What are antigenic properties?

Answer 1

Phenotype of the virus

Question 2

Is it easy to measure antigenic properties?

Answer 2

No it is hard
-Hard to get antiserum from a host that was recently infected
-Labor intensive
-Not precise

Question 3

Do all pathogens have genetic material?

Answer 3

Yes they either have DNA OR RNA

Question 4

True or false all NON-viruses have their genetic material encoded in RNA

Answer 4

False
-All non-viruses have their genetic material encoded in DNA

Question 5

Genome

Answer 5

Entire sequence of the genetic material of the organism

Question 6

Bases (RNA) /basepairs (DNA)

Answer 6

Measures genome size in the number of bases

Question 7

kilobase (kb)

Answer 7

-1,000 bp
-10^3

Question 8

Megabase (Mb)

Answer 8

-1,000,000 bp
-10^6 bp

Question 9

Gigabase (Gb)

Answer 9

-1,000,000,000 bp
-10^9

Question 10

Locus

Answer 10

Location in the genome

Question 11

Allele

Answer 11

A sequence at a locus

Question 12

How to calculate allele frequencies?

Answer 12

of specific type / total

Question 13

What do all the allele frequencies add up to?

Answer 13

1

Question 14

How do we visualize the sequences we extract from the genetic material of the samples?

Answer 14

Aligning sequences

Question 15

What does it mean to align 2 or more sequences

Answer 15

Find a correspondence/match between positions

Question 16

What is a gap?

Answer 16

Position only exists only in one sequence and not the other
-Insertion
-Deletion
-Sequencing error

Question 17

Mismatch

Answer 17

The bp changed due to a mutation or experimental error

Question 18

Match

Answer 18

The bp from each sequence are the same

Question 19

What is the principle of parsimony (Occam’s razor)

Answer 19

the simplest explanation or hypothesis that accounts for all the available evidence should be preferred over more complex or speculative ones.

Question 20

How can we evaluate how good an alignment is using the principle of parsimony?

Answer 20

Minimize the gaps, maximize the matches
-Mismatch/gap means there was evolutionary change which is more complex than saying there was no change (match)

Question 21

What is the ideal sequence we want from aligning them?

Answer 21

Highest number of matches