1. The main application of pairwise alignment is retrieving biological sequences in databases based on similarity.
a) true
b) false
Explanation: This process involves submission of a query sequence and performing a pairwise comparison of the query sequence with all individual sequences in a database. Thus, database similarity searching is pairwise alignment on a large scale. This type of searching is one of the most effective ways to assign putative functions to newly determined sequences.
2. Dynamic programming method is the fastest and most practical method
a) true
b) false
Explanation: Dynamic programming method is slow and impractical to use in most cases. Special search methods are needed to speed up the computational process of sequence comparison.
3. Which of the following is not one of the requirements for implementing algorithms for sequence database searching?
a) Size of the dataset
b) Sensitivity
c) Specificity
d) Speed
Explanation: There are unique requirements for implementing algorithms for sequence database searching out of which, the later three play an important role. However, speed can vary with the size of database. achieving all three at a time is nearly impossible.
4. Sensitivity refers to the ability to find as many correct hits as possible.
a) true
b) false
Explanation: Among the unique requirements for implementing algorithms for sequence database Searching, the first criterion is sensitivity, which refers to the ability to find as many correct hits as possible. It is measured by the extent of inclusion of correctly identified sequence members of the same family. These correct hits are considered ‘true positives’ in the database searching exercise.
5. The specificity refers to the ability to include incorrect hits
a) true
b) false
Explanation: In heuristic database searching methods, The second requirement criterion is 1 also called specificity, which refers to the ability to exclude incorrect hits. These incorrect hits are unrelated sequences mistakenly identified in database searching and are considered ‘false positives.’
6. In heuristic methods, speed doesn’t vary with the size of database.
a) true
b) false
Explanation: The speed is the time it takes to get results from database searches. Depending on the size of the database, speed sometimes can be a primary concern in the search methods.
7. An increase in sensitivity is associated with _______ in selectivity.
a) no specific change
b) increase
c) decrease
d) exponential increase
Explanation: Ideally, one wants to have the greatest sensitivity, selectivity, and speed in database searches. However, satisfying all three requirements is difficult in reality. What generally happens is that an increase in sensitivity is associated with decrease in selectivity. A very inclusive search tends to include many false positives. Similarly, an improvement in speed often comes at the cost of lowered sensitivity and selectivity. A compromise between the three criteria often has to be made.
8. Which of the following is incorrect?
a) Smith–Waterman algorithm is the fastest
b) Smith–Waterman algorithm is comparatively slower method
c) To speedup up comparison, heuristic methods are used
d) Heuristic algorithms perform faster searches
Explanation: Searching a large database using the dynamic programming methods, such as the Smith–Waterman algorithm, although accurate and reliable, is too slow and impractical when computational resources are limited. To speed up the comparison, heuristic methods have to be used. The heuristic algorithms perform faster searches because they examine only a fraction of the possible alignments examined in regular dynamic programming.
9. Currently, there are two major heuristic algorithms for performing database searches: BLAST and FASTA.
a) true
b) false
Explanation: These methods are not guaranteed to find the optimal alignment or true homologs, but are 50–100 times faster than dynamic programming. The increased computational speed comes at a moderate expense of sensitivity and specificity of the search, which is easily tolerated by working molecular biologists. Both programs can provide a reasonably good indication of sequence similarity by identifying similar sequence segments.
10. Which of the following is incorrect the ‘word’ method?
a) Both BLAST and FASTA use a heuristic word method
b) Word method is used for fast pairwise sequence alignment in BLAST and FASTA
c) The basic assumption is that two related sequences must have at least one word in common
d) Two related sequences must have at zero word in common while assuming
Explanation: This is the third method of pairwise sequence alignment. It works by finding short stretches of identical or nearly identical letters in two sequences. These short strings of characters are called words, which are similar to the windows used in the dot matrix method. The basic assumption is that two related sequences must have at least one word in common. By first identifying word matches, a longer alignment can be obtained by extending similarity regions from the words. Once regions of high sequence similarity are found, adjacent high-scoring regions can be joined into full alignment.