Bioinformatics Questions and Answers – Heuristic Database Searching

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This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Heuristic Database Searching”.

1. A main application of pairwise alignment is retrieving biological sequences in databases based on similarity.
a) True
b) False
View Answer

Answer: a
Explanation: This process involves submission of a query sequenceand performing a pairwise comparison of the query sequence with all individualsequences in a database. Thus, database similarity searching is pairwise alignmenton a large scale. This type of searching is one of the most effective ways to assign putativefunctions to newly determined sequences.
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2. Dynamic programming method is the fastest and most practical method.
a) True
b) False
View Answer

Answer: b
Explanation: Dynamic programming method is slow and impractical to use in most cases. Specialsearch 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 databasesearching?
a) Size of the dataset
b) Sensitivity
c) Specificity
d) Speed
View Answer

Answer: a
Explanation: There are unique requirements for implementing algorithms for sequence databaseSearching 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 manycorrect hits as possible.
a) True
b) False
View Answer

Answer: a
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 manycorrect 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
View Answer

Answer: b
Explanation: In heuristic database searching methods, The second requirement criterion is 1 also calledspecificity, which refers to the ability to exclude incorrect hits. These incorrect hits areunrelated sequences mistakenly identified in database searching and are considered ‘false positives.’
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6. In heuristic methods, speed doesn’t vary with the size of database.
a) True
b) False
View Answer

Answer: b
Explanation: The speed is the time it takes to get results from database searches. Depending on the size of the database, speed sometimes canbe 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
View Answer

Answer: c
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 improvementin 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
View Answer

Answer: a
Explanation: Searching a large database using the dynamic programming methods, such as theSmith–Watermanalgorithm, although accurate and reliable, is too slow and impracticalwhencomputationalresources are limited. To speed up the comparison,heuristic methods have to be used. The heuristic algorithms perform faster searchesbecause they examine only a fraction of the possible alignments examined in regulardynamic programming.

9. Currently, there are two major heuristic algorithms for performing databasesearches: BLAST and FASTA.
a) True
b) False
View Answer

Answer: a
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 andspecificity 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.
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10. Which of the following is incorrect the ‘word’ method?
a) Both BLAST and FASTA use a heuristic word method
b) Word method is usedfor fast pairwise sequencealignment in BLAST and FASTA
c) The basic assumption is that two relatedsequences must have at least one word in common
d) Two related sequences must have at zero word in common while assuming
View Answer

Answer: d
Explanation: This is the third method of pairwise sequence alignment. It works by findingshort 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 canbe joined into a full alignment.

Sanfoundry Global Education & Learning Series – Bioinformatics.

To practice all areas of Bioinformatics, here is complete set of 1000+ Multiple Choice Questions and Answers.

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Manish Bhojasia, a technology veteran with 20+ years @ Cisco & Wipro, is Founder and CTO at Sanfoundry. He is Linux Kernel Developer & SAN Architect and is passionate about competency developments in these areas. He lives in Bangalore and delivers focused training sessions to IT professionals in Linux Kernel, Linux Debugging, Linux Device Drivers, Linux Networking, Linux Storage, Advanced C Programming, SAN Storage Technologies, SCSI Internals & Storage Protocols such as iSCSI & Fiber Channel. Stay connected with him @ LinkedIn