Unit 1-Lecture 2 Flashcards
(21 cards)
What are antigenic properties?
Phenotype of the virus
Is it easy to measure antigenic properties?
No it is hard
-Hard to get antiserum from a host that was recently infected
-Labor intensive
-Not precise
Do all pathogens have genetic material?
Yes they either have DNA OR RNA
True or false all NON-viruses have their genetic material encoded in RNA
False
-All non-viruses have their genetic material encoded in DNA
Genome
Entire sequence of the genetic material of the organism
Bases (RNA) /basepairs (DNA)
Measures genome size in the number of bases
kilobase (kb)
-1,000 bp
-10^3
Megabase (Mb)
-1,000,000 bp
-10^6 bp
Gigabase (Gb)
-1,000,000,000 bp
-10^9
Locus
Location in the genome
Allele
A sequence at a locus
How to calculate allele frequencies?
of specific type / total
What do all the allele frequencies add up to?
1
How do we visualize the sequences we extract from the genetic material of the samples?
Aligning sequences
What does it mean to align 2 or more sequences
Find a correspondence/match between positions
What is a gap?
Position only exists only in one sequence and not the other
-Insertion
-Deletion
-Sequencing error
Mismatch
The bp changed due to a mutation or experimental error
Match
The bp from each sequence are the same
What is the principle of parsimony (Occam’s razor)
the simplest explanation or hypothesis that accounts for all the available evidence should be preferred over more complex or speculative ones.
How can we evaluate how good an alignment is using the principle of parsimony?
Minimize the gaps, maximize the matches
-Mismatch/gap means there was evolutionary change which is more complex than saying there was no change (match)
What is the ideal sequence we want from aligning them?
Highest number of matches
