Lec 6&7

Question 1

• is an evolutionary term.
• having common evolutionary origin

Answer 1

Sequence homology

Question 2

is a gene inherited in two species by a common ancestor.

Answer 2

homologous gene

Question 3

Homologous genes in different species performing the same function

Answer 3

orthologs

Question 4

aligns and compares two sequences along their entire length

Answer 4

global sequence-alignment

Question 5

algorithm that drives global alignment is?

Answer 5

Needleman Wunsch algorithm

Question 6

Global alignment works the best when the sequences are?

Answer 6

similar in character and length

Question 7

algorithm that drives local alignment is?

Answer 7

Smith-Waterman algorithm.

Question 8

Global Alignment
Suitable for similar and equal length sequences
T/F?

Answer 8

T

Question 9

Global Alignment
Suitable for partially similar, different length and conserved region containing sequences
T/F

Answer 9

F, Local Alignment

Question 10

useful in identifying conserved sequence segments across the sequences being aligned.

Answer 10

Multiple sequence alignments

Question 11

Identical amino acids are indicated by?

Answer 11

star (*)

Question 12

strongly and weakly similar substitutions are indicated by?

Answer 12

colon (:) and a dot (.).

Question 13

Specific combination of secondary structures organized into a characteristic three dimensional structure or fold.

Answer 13

Domains

Question 14

Groups of proteins that have the same domain arrangement or that are conserved along the whole sequence.

Answer 14

Families

Question 15

Structural units always found in two or more copies that assemble in a specific fold.

Answer 15

Repeats

Question 16

Region of domains containing conserved active or binding residues, or short conserved regions present outside domains that may adopt folded conformation only in association with their binding ligands.

Answer 16

Motifs

Question 17

Functional residues (active sites, disulfide bridges, post-translation modified residues).

Answer 17

Sites

Question 18

sequence found in the database, suspected as homologous

Answer 18

Hit

Question 19

allows a DNA or protein query sequence to be compared with sequences in the database.

Answer 19

BLAST algorithm

Question 20

searching is that homologous sequences are likely to contain a short, high-scoring similarity region.

Answer 20

main idea behind BLAST

Question 21

searches a nucleotide database using a nucleotide query

Answer 21

blastn

Question 22

searches a protein database using a protein query

Answer 22

blastp

Question 23

searches a protein database using a translated nucleotide query

Answer 23

blastx

Question 24

searches a translated nucleotide database using a protein query

Answer 24

tblastn

Question 25

searches a translated nucleotide database using a translated nucleotide query

Answer 25

tblastx

Question 26

(blastp) is useful in identifying these proteins.
T/F?

Answer 26

F, not useful

Question 27

is designed to detect weak relationships between the query sequence and other sequences in the database that are not necessarily detectable by standard BLAST searches.

Answer 27

(PSI-BLAST)

Question 28

is designed to search the database for proteins that are significantly related to the query sequence and also contain a pattern.

Answer 28

(PHI)

Question 29

searches for significantly similar sequences to both a query sequence and a signature.

Answer 29

PHI-BLAST

Question 30

is dependent on the database size and the query length.

Answer 30

E-value

Question 31

is the expectation value that indicates the number of alignments with a score ≥S that one can expect to find by chance in a database of size N.

Answer 31

E-value

Question 32

bit score is dependent on?

Answer 32

sequence length