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Lecture 11

Biology 2581B Lecture Notes - Lecture 11: Sequence Database, Single-Nucleotide Polymorphism, Sanger Sequencing


Department
Biology
Course Code
BIOL 2581B
Professor
Susanne Kohalmi
Lecture
11

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Genetics Lecture 11 Notes
Uniqueness of DNA sequence:
In short space DNA can store lots of information
o How can we see this properly?
o How long does a DNA sequence have to be for us to expect that it is
unique in a genome?
o Have a high probability of occurring once?
o Basis for computer searches.
If A=T=G=C what are the sequence permutations of a sequence 1 base long?
o It has equal probability of being A, T, G, or C, therefore 4 permutations
o ¼ chance that the base is A
o Chance of particular sequence = 1/sequence permutations
If the sequence is 2 bases long, what is the chance that is has the sequence GT?
o (1/4)^4 = 1/16
o In the case of A = T = G = C
o 1/sequence permutations = ¼4 (n=length)
How many total positions are there of that length within
the genome? How many positions are there within genomes?
The e^-381 is the change that this sequence
does not occur in the genome

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There is a good chance that you wouldn’t
find this sequence within a genome. The larger the sequence, the smaller the chance
you will find it in the genome.
Individual events so just multiply the probability
of each event occurring (0.37^2)
Overall…
Short sequences of 50 bases are not expected to occur at random in the
sequence database
Therefore, if you take a 50 base sequence from a mouse and found that it
existed in humans, there is a significant, non-random find
o Would not expect same sequence to be in both a human & a mouse if
it is, this is a non-random find 2 sequences are related
because if they weren’t, you wouldn’t expect it to happen
Sequencing the human genome 3 maps:
1. High resolution genetic map
2. Physical map
3. Sequence map
Human genetic map was not very good in the 1980s
o Had mistakes, was not done systematically
o Used sequence base mapping looked for SNPs (single
nucleotide polymorphisms) as a marker
o Also used simple sequence repeats variation in # of
repeats
Creating a high resolution linkage map:
Large scale efforts to find SNPs and SSRs to create a high
resolution linkage map
Provide landmarks to orient the physical and sequence maps
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