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What is a locus?
What is a SNP?
A location in the genome; it can be a single nucleotide site or a stretch of many nucleotides.
The DNA or gene variant that one notices in a comparison of sequences in a populations.
What is a microsatellite loci?
What is an example?
Are loci that have a short sequence motif, 2 to 6 base pairs long, that is repeated multiple times with different alleles having different numbers of repeated.
2bp sequence motif AG at a locus might tenderly repeat 5 times in one allele and 2 time in another.
What are common SNPs?
What are rare SNPs?
Are SNPs in a population if the less common allele is 5% or greater.
Are SNPs in a population if the less common allele is 5% or less
What are the SNPs within protein-coded regions are classified into?
What are their definitions?
- Synonymous is when the different alleles code for same amino acids.
- Nonsynonymous is when the two alleles encode for different amino acids.
- Nonsense is when one allele encodes for a stop codon and the other an amino acid.
What is a silent SNP?
What are they useful for?
What can they be used as?
Is an SNP that is located outside of coding sequences.
In population genetics even if they are found in nonfunctional DNA since they can be used as markers to address question about population-genetic processes such as gene flow between populations.
or to study gene flow in population genetics.
What is a genotype?
Once SNPs have been discovered, what can be determined at each SNP?
What technology used for this that contains thousands of probes corresponding to known SNPs?
It is the allelic composition.
The genotype (allelic composition) of different individuals in the population.
How does the Microarray work?
- 1. An array of DNA fragments representing all the genes in a genome are glued to the surface of a postage-stamp-size slide.
- 2. The microarray is bathed into the SNPs (labeled probe that has fluorescent tags).
- 3. Transcribed regions with fluoresce and show which region is homozygous or heterozygous based on color.
Why are micro satellites more powerful loci for population genetic analysis?
1. More alleles per locus (20 or more compared with no more than 4 in SNPs).
2. Higher mutation rates (10^-2 to 10^-6 per locus per generation) than SNPs (2x10^-8) per locus per generation.
3. Microsatellites are more common in genomes.
What does higher mutation rate and more alleles per locus in micro satellites mean?
- Higher variation levels, different individuals are more likely to have:
- 1. Different genotypes
- 2. More alleles per locus
Where are micro satellites with tri-nucleotide repeats found?
What do they encode for?
In coding regions.
String of amino acids.3
What are the two main methods for detecting micro satellite loci?
What happens after the micro satellite and the flanking sequences have been identified?
If the complete genomic sequence is present, then use a computer.
One creates a genomic library, screens the library with a probe for motive of interest (As and Cs), and determine the DNA sequence of the clone and the sequences that flank them.
DNA samples from individuals in a population can be analyzed to determine the number of repeats that that are in an individual.
What are the different types of haplotype variations in a population that can be analyzed?
What is the insertion-deletion polymorphism?
- Inversions, translocations, inversions, deletions, or duplications.
- Presence or absence of a transposable elements at a particular locus in the genome
It is indel, it is the type of polymorphism that involves the presence or absence of one or more nucleotides at a locus in one allele relative to another.
What is a frameshift mutation?
What is an example?
A frameshift mutation is the genetic mutation caused by indels in the DNA sequence that shifts the way the sequence is read.
An example is the myostatin gene that causes the protein in dogs to be truncated giving rise to a Whippet with a single mutation (mh/+), dog runs faster and is buff. But (mh/mh) genotypes give dogs with disabling muscle cramps.
On average, there is a SNP every how many base pairs?
So most SNPs fall within genes? If no, then where? Some can be what?
- No, most SNPs fall within non-functional regions.
- Some can be enhancers.
What is an easy way to genotype alleles at each marker?
Measuring the genotype length differences.