1. When did Needleman-Wunsch first describe the algorithm for global alignment?
a) 1899
b) 1970
c) 1930
d) 1950
Explanation: Needleman and Wunsch were among the first to describe dynamic programming algorithm for global sequence. In global sequence alignment, an attempt to align the entirety of two different sequences is made, up to and including the ends of sequences.
2. Which of the following does not describe dynamic programming?
a) The approach compares every pair of characters in the two sequences and generates an alignment, which is the best or optimal
b) Global alignment algorithm is based on this method
c) Local alignment algorithm is based on this method
d) The method can be useful in aligning protein sequences to protein sequences only
Explanation: The method can be useful in aligning nucleotide to protein sequences as well. These programs first perform pair-wise alignment on each pair of sequences. Then, they perform local re-arrangements on these results, in order to optimize overlaps between multiple sequences.
3. Which of the following is not an advantage of Needleman-Wunsch algorithm?
a) New algorithmic improvements as well as increasing computer capacity make it possible to align a query sequence against a large DB in a few minutes
b) Similar sequence region is of same order and orientation
c) This does not help in determining evolutionary relationship
d) If you have 2 genes that are already understood as closely related, then this type of algorithm can be used to understand them in further details
Explanation: Needleman-Wunsch algorithm is used when 2 genes that are already understood as closely related and can be used to understand them in further details. This is quite helpful in finding orthologs, paralogs and homologs in evolutionary studies.
4. Which of the following is not a disadvantage of Needleman-Wunsch algorithm?
a) This method is comparatively slow
b) There is a need of intensive memory
c) This cannot be applied on genome sized sequences
d) This method can be applied to even large sized sequences
Explanation: This method cannot be applied on genome sized sequences. But this is indeed useful in determining similarities and evolutionary relationships.
5. Which of the following does not describe global alignment algorithm?
a) In initialization step, the first row and first column are subject to gap penalty
b) Score can be negative
c) In trace back step, beginning is with the cell at the lower right of the matrix and it ends at top left cell
d) First row and first column are set to zero
Explanation: Initialization and scoring system of the Smith–Waterman algorithm and Needleman-Wunsch algorithm is quite different. In global alignment first row and first column are subject to gap penalty and are not set to 0.
6. Which of the following does not describe PAM matrices?
a) These matrices are used in optimal alignment scoring
b) It stands for Point Altered Mutations
c) It stands for Point Accepted Mutations
d) It was first developed by Margaret Dayhoff
Explanation: PAM stands for Point Accepted Mutations. PAM matrices are calculated by observing the differences in closely related proteins. One PAM unit (PAM1) specifies one accepted point mutation per 100 amino acid residues, i.e. 1% change and 99% remains as such.
7. Which of the following is untrue regarding the scoring system used in dynamic programming?
a) If the residues are same in both the sequences the match score is assumed as +5 which is added to the diagonally positioned cell of the current cell
b) If the residues are not same, the mismatch score is assumed as -3
c) If the residues are not same, the mismatch score is assumed as 3
d) The score should be added to the diagonally positioned cell of the current cell
Explanation: If the residues are not same, the mismatch score is assumed as -3 and it has to be negative. However, these scores are not unique, they can be user defined also, but the mismatch and gap penalty should be the negative values.
8. Which of the following does not describe global alignment algorithm?
a) Score can be negative in this method
b) It is based on dynamic programming technique
c) For two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1
d) For two sequences of length m and n, the matrix to be defined should be of dimensions m and n
Explanation: For two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1so that there is margin for addition of the score along the diagonal. Also, corresponding score is further calculated at the end cumulatively.
9. Which of the following does not describe global alignment algorithm?
a) It attempts to align every residue in every sequence
b) It is most useful when the aligning sequences are similar and of roughly the same size
c) It is useful when the aligning sequences are dissimilar
d) It can use Needleman-Wunsch algorithm
Explanation: Performing global alignment is most useful when the aligning sequences are similar and of roughly the same size. This is most useful to find the similarities among the organisms that are roughly connected on the timeline.
10. Which of the following is wrong in case of substitution matrices?
a) They determine likelihood of homology between two sequences
b) They use system where substitutions that are more likely should get a higher score
c) They use system where substitutions that are less likely should get a lower score
d) BLOSUM-X type uses logarithmic identity to find similarity
Explanation: BLOSUM-X type identifies sequences that are X% similar to the query sequence i. e. score 54 corresponds to 54% similarity hence reducing the complexity of the output and giving the similarity in percentage. Also, these matrices are popular in bioinformatics due to their speed and accuracy.