Applied bioinformatics

Question 1

orthologs

Answer 1

proteins from different species, evolved by vertical descend (speciation), typically retain same function as original

Question 2

paralogs

Answer 2

proteins within a given species, derived from gene duplication, may evolve new functions that are related to the original

Question 3

describe the fasta format

Answer 3

> ID text sequence

Question 4

biological importance of alignment

Answer 4

sequence alignments assess degree of similarity between sequences

Question 5

what does sequence similarity suggest?

Answer 5

evolutionary history

Question 6

molecular clock principle

Answer 6

fewer differences - more recent divergence (assumption that number of mutations reflects time of evolution)

Question 7

scoring matrices

Answer 7

quantify quality of alignments

Question 8

what do the two most important scoring matrices score for?

Answer 8

• similar structural domains (BLOSUM)

- evolutionary relationships (PAM)

Question 9

what is the approach of PSI-Blast?

Answer 9

iterative approach to searching: increase sensitivity by using previous results in the next iteration

Question 10

what can often be a source of error in iterative approaches?

Answer 10

inclusion of an unrelated sequence from a previous iteration may lead to more accumulation of unrelated sequences in subsequent iterations

Question 11

what is the most commonly involved mutation in a hereditary predisposition for cancer?

Answer 11

inheritance of a defect tumor suppressor gene