Name different types of DNA sequence variations.
Single nucleotide polymorphisms (SNPs)
most common type of variation in humans (90% of variation)
Simple tandem repeat polymorphisms (STRs)
Insertions/Deletions (indels)
Why is understanding genomic variance substantial for research? (DNA variants)
direct trace of heritable traits
biomarkers
health & medicine —> diseases
forensics —> identification
human evolution
Do SNPs mostly occur in coding or non-coding sequences?
can occur everywhere
mostly non-coding
if coding: of great interest -> could alter the resulting protein (-> Ka/Ks)
How can you discover polymorphisms in DNA?
—> DNA sequencing and comparison
Name two tools that can be used to analyze SNPs.
PolyPhen
SIFT (sort intolerant from tolerant substitutions)
Outline the general procedure of SIFT.
search for similar sequences (BLAST)
choose closely related sequences that may share a similar function
obtain multiple alignments
calculate normalized probabilities for all possible substitutions at each position
—> Substitutions with a very low probablity = deleterious, other = tolerated
—> relatively fast and easy -> filter for SNPs that require in-depth analysis
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