Bioinformatics

Question 1

chromosomal microarray

Answer 1

looks for deletions and duplications

Question 2

transition

Answer 2

change from one purine to another purine (A>G) or the change from one pyrimidine to another (C>T)

Question 3

transversion

Answer 3

the change from a purine to a pyrimidine (A >T) or change from pyrimidine to a purine (C>G)

Question 4

define identity

Answer 4

the extent to which two sequences (nts or AAs) hav the same residues at the same positions in an alignment = expressed as a percentage

Question 5

define similarity

Answer 5

extent to which nucleotide and protein sequences are related
- similarity between two sequences can be expressed as percent sequence identity and/or percent positive substitutions

Question 6

homologs

Answer 6

Similarity to nucleotide or protein that can be attributed to a common ancestor

Question 7

orthologs

Answer 7

types of homologs present in different species that arise from same ancestor; Similar sequences but different functions; may or may not have same function but same origin

Question 8

paralogs

Answer 8

result of gene duplication from early ancestor; very early on globin gene diverged to become alpha and beta

Question 9

alignment types (2)

Answer 9

global = align the complete sequences

local = identify only the most similar segments or sequence patterns (motifs)

Question 10

dynamic programming

Answer 10

best but takes a while
quick good answer = heuristic

Question 11

T or F. Transversions happen more than transitions

Answer 11

F! Transitions happen more frequently than transversions
= often desirable to score these substitutions differently

Question 12

simple scoring matrix

Answer 12

match = 5
gap = 1
transition = 3
transversion = 2

Question 13

BLAST

Answer 13

Basic Local Alignment Search Tool

• finds regions of similarity between biological sequences
• program compares nucleotide or protein sequences to sequence databases and calculates the statistical difference

Question 14

Blast E-value

Answer 14

the number of expected hits of similar quality (scoe) that could be found just by chance

E- value of 10 = up to 10 hits can be expected to be found just by chance, given the same size of a random database

the smaller the E-value, the better the match!

Question 15

megablast

Answer 15

default
for sequence ID, intra-species comparison

Question 16

blastn

Answer 16

for searching with shorter queries, cross-species comparison

Question 17

discontiguous megablast

Answer 17

for cross species comparison

Question 18

T or F. BLAST is a heuristic alignment algorithm

Answer 18

T!

Question 19

T or F. The lower the E-value, the more likely that two sequences are related

Answer 19

T!

Answer 20

carat
- site between 2 adjoining nucleotides, such as restriction enzyme site, is indicated by listing the to points separated by a carat
- n^n+1 = 55^56 (between 55 & 56, sequence cut there)