You are carrying out a pairwise alignment of two long aminoa

You are carrying out a pairwise alignment of two long amino-acid sequences of a shark and a human, representing species that split from each other hundreds of millions of years ago, with similarities of about 30%. You decide to use a PAM matrix. Which PAM matrix should you use?

PAM 40

PAM 100

PAM 250

4 points   

QUESTION 2

If we are interested in looking at the correlation of genetic variants with some particular condition or disease we would need to use __________ markers

Monomorphic

Polymorphic

Anamorphic

Fixed

4 points   

QUESTION 3

A PCR-based marker that amplifies a unique region of a genome is known as a __________.

EST

GDB

STS

STR

4 points   

QUESTION 4

The two sequences below have been aligned. Calculate to score for this pairwise alignment, given a match score of 0, a mismatch score of 1, a gap cost of 5, and a gap-extension cost of 1
TAACCAGCTTTTCT,TTACAGCGGTCTTTCT

-TAACCAGCT---TTTCT
T..--....GGTC.....

19

22

23

27

4 points   

QUESTION 5

The number that uniquely identifies each GenBank record is the:

Primary number

Accession number

Identity number

Catalog number

4 points   

QUESTION 6

RefSeq is an example of a __________ database.

Curated

Secondary

Annotated

All of the above

4 points   

QUESTION 7

The Needleman-Wunsch algorithm is guaranteed to find the optimal alignment of a pair of sequences, given a set of costs.

True

False

4 points   

QUESTION 8

If you are annotating a sequence to submit to GenBank, you would put the information about open reading frames or Coding sequences in the __________ field.

Keywords

Reference

Features

Locus

4 points   

QUESTION 9

Variation at a particular nucleotide site giving rise to two different bases at that site is another type of genetic marker known as a __________.

VNTR

SNP

STR

STS

4 points   

QUESTION 10

Comparisons of sequences between organisms that are inherited from a common ancestral sequence, and which have not undergone gene duplication events are called __________.

Orthologous

Paralogous

Semi-conserved

Ancestral

4 points   

QUESTION 11

The following is an example of a __________ file format.

>AY138125
TGACCTGTTCAACACGAACGCGGCCATCGTGCGTGACCTGAC

GenBank

EMBL

DDBJ

FASTA

4 points   

QUESTION 12

Comparisons of sequences between organisms that are inherited from a common ancestral sequence, and which have undergone gene duplication events as well as speciation events are called __________.

Orthologous

Paralogous

Semi-conserved

Ancestral

4 points   

QUESTION 13

Databases into which raw nucleotide or amino-acid sequences are deposited are called __________ databases.

Primary

Secondary

Tertiary

Initial

Experimental

		PAM 40
		PAM 100
		PAM 250

Solution

Question 1
Correct answer : PAM 250
Explanation : PAM 250 is used for 15% - 30% similarity
PAM 40 is used for 75% - 75% similarity
PAM 100 is used for 60% similarity

Question 2
Correct answer : Polymorphic
Explanation : Every living organism bears some unique sequence which makes then unindentical with the rest of the otheres. This is called SNP or single nucleotide polymorphism. To detect these genes we need a polymorphic marker.