Sequence alignment (long ver p2)

Question 1

Examples of Pairwise alignment software

Answer 1

EMBL - EBI Pairwise Sequence Alignment
BLAST’

Question 2

What are the different applications of Pairwise Alignment?

Answer 2

measuring sequence similarity
studying the evolution of sequences

Question 3

share a common evolutionary ancestor

Answer 3

Homologous sequences

Question 4

True or False: Homologous sequences does not share a significantly related 3D structure but share the same evolutionary ancestor

Answer 4

False

shares the same 3D structure

Question 6

usually share significant amino acid/ nucleotide identity

Answer 6

homologous sequences

Question 7

sequence regions that are homologous are also called

Answer 7

conserved regions

Question 8

sequences that share a common evolutionary ancestry

Answer 8

homologs

Question 9

derived from a single ancestral gene in the last common ancestor

Answer 9

orthologs

Question 10

homologous genes with identical function in different organisms and is only separated by speciation

Answer 10

orthologs

Question 11

two or more homologous genes found within a single species

Answer 11

paralogs

Question 12

separated by a gene duplication event

Answer 12

paralogs

Question 13

if a gene in an organisms is duplicated and transposed so that two copies occupy two different positions in the same genome, then the two copies are _

Answer 13

paralogous

Question 14

create gene families

Answer 14

paralogs

Question 15

consists of two or more copies of paralogous genes within the genome of a single organism

Answer 15

gene families

Question 16

True or False: Biological sequences does not occur in families

Answer 16

False

it often occurs in families

Question 17

related genes within an organism

Answer 17

paralogs

Question 18

sequences within a population

Answer 18

polymorphic variants

Question 19

genes in other species

Answer 19

orthologs

Question 20

True or false: Homologous sequences often retain similar structures and functions

Answer 20

True

Question 21

collection of three or more proteins (or nucleic acid) sequences that are partially or completely aligned

Answer 21

multiple sequence alignment

Question 22

Homologous residues are aligned in _ across the length of the sequences

Answer 22

columns

Question 23

In multiple sequence alignment, the residues are presumed to be homologous in an:

Answer 23

evolutionary and structural sense

Question 24

residues are homologous as they are presumably derived from a common ancestor

Answer 24

evolutionary sense

Question 25

aligned residues tend to occupy corresponding positions in the three-dimensional structure of each aligned protein

Answer 25

structural sense

Question 26

What are the 5 main approaches to multiple sequence alignment

Answer 26

exact methods progressive alignment iterative approaches consistency-based methods structure-based methods

Question 27

employs dynamic programming (similar to Needleman Wunsch but the matrix is multidimensional)

Answer 27

exact methods

Question 28

goal is to maximize the summed alignment score of each pair of sequences

Answer 28

exact methods

Question 29

generate optimal alignments but are not feasible in time or space for more than a few sequences

Answer 29

exact methods

Question 30

strategy entails calculating pairwise sequence alignment scores between all the proteins (or nucleic acid sequences) being aligned

Answer 30

Progressive Sequence Alignment

Question 31

beginning the alignment with 2 closest sequences and progressively adding more sequences to the alignment

Answer 31

progressive sequence alignments

Question 32

What is the pro of Progressive Sequence Alignment?

Answer 32

permits rapid alignment of hundredsthousands of sequences

Question 33

What is the con of Progressive Sequence Alignment?

Answer 33

final alignment depends on the order in which sequences are joined; not guaranteed to provide most accurate alignments

Question 34

What are the examples of Progressive Sequence Alignment?

Answer 34

ClustalIW

Question 35

What are the 3 stages of ClustalIW algorithm?

Answer 35

STAGE 1: create pairwise alignment of every protein included in MSA STAGE 2: guide tree is calculated from the distance (similarity) matrix STAGE 3: MSA is created based on guide tree

Question 36

two ways to construct guide tree

Answer 36

Unweighted Pair Group Method of Arithmetic Averages (UPGMA) Neighbor-Joining Method

Question 38

compute a suboptimal solution using a progressive alignment strategy, and then modify the alignment using dynamic programming or other methods until a solution converges

Answer 38

Iterative Approaches

Question 39

What is the advantage of Iterative Approach over Progressive Sequence Alignment?

Answer 39

overcome alignment errors by iterative refinment

Question 40

What is an example of Iterative Approach?

Answer 40

MAFFT

Question 41

What does MAFFT mean?

Answer 41

Multiple Alignment using Fast Fourier Transform

Question 42

example of multiple alignment package that is considered to be highly accurate based on recent benchmarking studies

Answer 42

MAFFT

Question 43

use information about the multiple sequence alignment as it is being generated to guide the pairwise alignments

Answer 43

consistency-based methods

Question 44

example of Consistency-based approach

Answer 44

T-coffee

Question 45

What does t-coffee mean

Answer 45

tree-based consistency objective function for alignment evaluation

Question 46

include all possible pairwise global alignments of the input sequences and the 10-highest scoring local alignments

Answer 46

T-coffee

Question 47

True or False: every pair of aligned residues is assigned a weight

Answer 47

T-coffee

Question 48

based on the idea that the tertiary structures evolve more slowly than primary sequences

Answer 48

structure-based approaches

Question 49

accuracy of msa is improved by including information about the 3-dimensional structure of one or more members of the group of proteins being aligned

Answer 49

structure-based approaches

Question 50

a compilation of both multiple sequence alignments and profil HMMs of protein families

Answer 50

Pfam

Question 51

What does Pfam mean?

Answer 51

Protein Family Database of Profile HMMs