Lecture 14 Flashcards
Where were the loci responsible or the behaviour of the dogs?
they hah whole genome sequences for over 1000 dogs and identified the top associated loci for each lineage, most alleles that changed PT could be found in all dogs and non-zero frequencies in wolves
found in non-coding
Photo 5
What was the goal?
What did they fund?
Goal was to find loci in sheepdogs that differed from all other dogs
Found SNP loci where allele frequency’s is significantly different
How might one detect selection or non-neutrality at synonymous sites?
dn/ds
Where is the synonymous and non-syn parts in photo 6
The third position is the synonymous site and a mutation here would not been seen becuase of purifying selection
dn/ds=1=
dn/ds>1.0=
dn/ds<1.0=
=random or neutral selection
=positive selection change at non-sun faster then syn.
=purifying selection synonymous are evolving neutrally
If synonymous site are not evolving neutrally, that’s a problem for that formula. How could we test that this?
ds/di
compared to changes in the intron
Photo 7- Widespread POsitive Selection in Synonymous Sites of Mammalian Genes
-explain
-1562 rats and mouse orthologous( homologous genes where a gene diverages after a speciation event) pairs
-aligned introns that occur between exons that are 80% identical at the AA level
-remove first intron which often plays a role in transcription regulation
Explain photo 7 for 1562 rodents
Ki is introns
ki and ks have similar peaks therefore evolving at the same speed
Photo 8
give percentages of colour curves
a)non-syn
b)syn.
d)intron
blue 28% show purifying selection at syn sites compare b and d
red 12% positive selction(syn sites evolving faters than intron sites)
Green 60% Ks and Ki-psuedo were similar(syn neutral)
Photo 8
there appear to be contraints on codon usgae for almost a ____
third of the genes
Rare codons are more common in genes with_____rates in several genomes, including humans
low translation
in mammals synonymous sites within the first are more GC-rich then the last exons(coding) of the genes, relevant to translation regualtions, whereas theire is______
no difference between GC contents of first ans last introns of genes(non-coding)
Why does Escherichia coli accept aminoacyl-tRNA rather then rare codons?
shabalina
Common codons can increase the rate of translation elongation serval folds
What does BLAST stand of?
Basic Local Alignment Search Tool
What is BLAST used for?
USed to identify homologous sequences. Homologous sequences include duplicates within genomes(paralogs) which allows us to study gene duplication and divergence
