Lecture 2 DA Flashcards
What is a blast search?
A sequence alignment.
What is checked for in a protein when a sequence is found (4)?
Whether the protein is:
- known, with known function
- known, but with unknown function
- novel, but with known similar sequences of known function
- novel, with no known similar sequences
Does high similarity necessitate actual similarity? Why/why not?
No, because they could be similar due to convergent evolution.
What is homology?
Descent from a common ancestor.
What is orthology?
Descent from speciation event.
What is paralogy?
Descent from duplication event.
What is xenology?
Descent from horizontal transfer event.
What percentage of identical amino acids is required for two proteins to have similar folding patterns? What is the most likely relation between them, and what does this depend on?
> 25%. They’d most likely be homologous. Depends highly on e-value.
What percentage similarity of identical amino acids between two proteins is the twilight zone for determining similar folding patterns?
18-25%.
What percentage similarity of identical amino acids between two proteins means similar folding patterns by a sequence alignment cannot be determined?
What does the e-value represent?
Measure of the chance of obtaining the result by random.
What is more informative, amino acid/primary sequence alignment, or a nucleic acid alignment?
Protein, as it involves 20 characters, vs 4.
What does the e-value represent?
Measure of the chance of obtaining the result by random.
What is more informative, amino acid/primary sequence alignment, or a nucleic acid alignment?
Protein, as it involves 20 characters, vs 4.
What is rarer: insertion of a gap, or the exchange of a nucleotide? What consequence does this have on the scoring system?
Insertion of a gap. Therefore, a bigger penalty on inserting gaps.
