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In accordance with the Coursera Honor Code, I (Anonymous Student) certify that the answers here are my own work.

Question 1

The PAM 50 substitution matrix is derived in which of the following ways:

The matrix is based on short term mutation rates, mathematically extrapolated by 50 matrix multiplications.

The matrix is based on the mutation rate is sequences that are 50% identical.

The matrix is is based on pairwise mutation rates multiplied by 50 to generate whole numbers.

The matrix is based on actual amino acid changes in proteins that are, at most, 50% identical.

Question 2

If the search space is 31 bits, then what is the E value of a sequence match with an adjusted score (S') of 28. ______________

Question 3

In a database search, one of the hits in the output has a score (S') of 27 bits and an E value of 0.54. Which of the following statements is correct?

It must be a homolog because the E value is less than 1.

The score is too low and the E value is too high--it is not a homolog.

The size of the database is 27 bits.

Although the E value is too high to call it a homolog, non-homology should not be inferred

Question 4

What is the best parameter for assessing homology of a query protein to a protein found in a database search?

raw score

% identity

E value

% similarity

Question 5

You run a PSI-BLAST and one of the hits in the second iteration has an E value of 3e-17. What is the best description of your conclusion?

It can only be homologous to the query if it is 10% identical.

It is clearly homologous to the query sequence, because its E value is less than 1e-04.

It is a putative homolog of the query sequence and further investigation is needed to confirm.

It may not be homologous to the query sequence, but it is clearly a member of the protein family seen in the PSSM.

Question 6

You start with a query protein and successfully find a putative homolog from pig but only on the third iteration of PSI-BLAST. The putative homolog proves to be an actual homolog based on structure data. Why might BLAST have not found this homolog on the initial iteration?

BLAST uses a global alignment strategy that is not suited for finding local regions of similarity.

BLAST is not 100% sensitive in finding all homologs in a database.

Pig proteins are all hypothetical sequences.

It must be so distantly related that any alignment program could not have picked up the homology.

Question 7

Analyze the following BLAST result (E value is on the far right):

Sequences producing significant alignments: (Bits) E Value
gi|130346|sp|P07863|PMEA_ERWCH Pectinesterase A precursor (Pecti 99.8 7e-21
gi|2507166|sp|P46130|YBHC_ECOLI Acyl-CoA thioester hydrolase ybg 45.1 2e-04
gi|1168712|sp|P46081|BXCN_CLOBO Botulinum neurotoxin type C1, no 33.1 0.79
gi|547993|sp|P37060|NANH_VIBCH Sialidase precursor (Neuraminidas 30.4 5.1

The Pectinase A precursor is not homologous to the query sequence.

No conclusions can be made regarding homology between the Pectinase A precursor and the query sequence.

BLAST is insufficient in assessing homology.

The Pectinase A precursor is homologous to the query sequence.

Question 8

The Botulinium neurotoxin is not homologous to the query sequence.

BLAST is insufficient in assessing homology.

No conclusions can be made regarding homology between the Botulinum neurotoxin and the query sequence.

The Botulinum neurotoxin is homologous to the query sequence.

Question 9

BLAST is the Basic Local Alignment Search Tool. Why is local pairwise alignment essential for BLAST?

To find related sequences in a database, a query sequence must be able to be effectively aligned with the sequences in that database.

FASTA must be run prior to running BLAST.

PSI-BLAST must be used for this.

Database sequences must be aligned with each other in every possible combination.

Question 10

Which of the following is NOT possible for a pair of aligned sequences?

10% identity, 20% similarity

40% identity, 15% similarity

10% identity, 30% similarity

49% identity, 51% similarity

In accordance with the Coursera Honor Code, I (Anonymous Student) certify that the answers here are my own work.

You cannot submit your work until you agree to the Honor Code. Thanks!

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