Sequence alignment (long ver p1)

Question 1

DNA Alphabet aside from ATGC

B

Answer 1

C, G, T

Question 2

DNA Alphabet aside from ATGC

D

Answer 2

A, G, T

Question 3

H

Answer 3

A, C, T

Question 4

K

Answer 4

G, T

Question 5

M

Answer 5

A, G

Question 6

N

Answer 6

A, C, G, T

Question 7

R

Answer 7

A, G

Question 8

S

Answer 8

C, G

Question 9

V

Answer 9

A, C, G

Question 10

W

Answer 10

A, T

Question 11

Y

Answer 11

C, T

Question 12

What are the different biological sequences?

Answer 12

Nucleic Acid
Protein / Amino Acid

Question 13

amino acid code is a _

Answer 13

one letter abbreviation

Question 14

Enumeration

What is the significance of Sequence Alignment?

Answer 14

learn about gene or protein through homology
discover functional, structural, and evolutionary information of sequences
obtain best possible/”optimal”alignment using algorithms

Question 15

process of lining up two sequences to achieve maximal levels of identity and show conservation of residues

Answer 15

pairwise alignment

Question 16

way to represent the relationship between two biological sequences (proteins or nucleotides)

Answer 16

pairwise alignment

Question 18

used to assess degree of similarity and possibly homology

Answer 18

pairwise alignment

Question 19

same residues between two proteins; may be in global or local alignment

Answer 19

identical

Question 20

residues have structural or functionally related

Answer 20

similar

Question 21

can only use ‘higher/lower’degree of similarity

Answer 21

similar

Question 22

sum of both identical and similar residues

Answer 22

percent similarity

Question 23

goal of pairwise alignment

Answer 23

percent similarity

Question 24

refers to an exact match between two nucleotides or amino acids

Answer 24

identity

Question 25

refers to a resemblance between two residues that is greater than one would expect at random

Answer 25

similarity

Question 26

simple picture that gives an overview of the similarities between two sequences

Answer 26

dot plot

Question 27

what correspond to the residues of dot plot?

Answer 27

rows and columns

Question 28

positions in the dot plot are _ if the residues are different, and _ if they match

Answer 28

left blank - different filled - match

Question 29

compare sequences as a whole

Answer 29

global alignment

Question 30

no amino acids or nucleotides is discarded

Answer 30

global alignment

Question 31

It is used when sequences are quite similar and approximately the same length

Answer 31

global alignment

Question 32

analyze polymorphisms between closely related sequences

Answer 32

global alignment

Question 33

What kind of algorithm does Global alignment use?

Answer 33

Needleman Wunsch algorithm

Question 34

stretches of sequence with high density of matches are aligned (generate islands of matches)

Answer 34

local alignment

Question 35

more suitable for aligning sequences that are similar in some regions (maybe a conserved region or domain) but different in others

Answer 35

local alignment

Question 36

detect similar subsequences in two sequences

Answer 36

local alignment

Question 37

What is the algorith used in Local Alignment?

Answer 37

Smith Waterman algorithm

Question 38

What are the steps in Pairwise Comparison?

Answer 38

Set up the matrix Score the matrix Identifying the optimal alignment

Question 39

How to set up the matrix?

Answer 39

one sequence is written left right/ top bottom; one residue at a time

Question 40

# Scoring the matrix protein

Answer 40

Choose PAM or BLOSUM Choose number

Question 41

# Scoring the matrix DNA

Answer 41

score for identities or mismatches

Question 42

What does PAM mean?

Answer 42

Percent Accepted Mutation

Question 43

estimates the rate at which each possible residue in a sequence changes to each other residue over time

Answer 43

PAM

Question 45

What does BLOSUM-X means?

Answer 45

Blocks Amino Acid Substitution Matrix

Question 46

Amino acids are grouped according to the chemistry of the side group

Answer 46

Substitution Matrix: PAM

Question 47

# Log odd values +10

Answer 47

means that ancestor is probability is greater

Question 48

# Log odd values 0

Answer 48

means that the probability are equal

Question 49

# log odd values 4

Answer 49

means that the change is random

Question 50

True or False: Substitution Matrix: BLOSUM is not based on an explicit evolutionary model

Answer 50

True

Question 51

derived from all amino acid changes observed in an aligned region given a family of proteins regardless of the protein's sequence similarity but are related biochemically (basis of common ancestor)

Answer 51

Substitution matrix: BLOSUM

Question 52

Matrix is based on substitutions and conserved positions in BLOCKS

Answer 52

Substitution matrix: BLOSUM

Question 53

common regions in related sequences

Answer 53

blocks

Question 54

used to find conserved domains

Answer 54

Substitution matrix: BLOSUM