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Bioinformatics Practice Test Questions: Multiple Sequence Alignment (MSA)
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Multiple sequence alignment (MSA) is a tool used to identify the evolutionary relationships and common patterns between genes.

Topics include: Exhaustive Algorithms, Heuristic Algorithms, Needleman – Wunsch Algorithm, Progressive Methods of Multiple Sequence Alignment, Iterative Methods of Multiple Sequence Alignment, Localized Alignments in Sequences, Statistical Methods for Aiding Alignment, & Position – Specific Scoring Matrices.

Bioinformatics Practice Test Questions: Multiple Sequence Alignment (MSA)
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25 Questions

1. The number of possible global alignments between two sequences of length N is _____
2. Which of the following is untrue regarding T-Coffee?
3. Which of the following is untrue about iterative approach?
4. MACAW is a local multiple sequence alignment program only.
5. In a multidimensional search matrix, for aligning N sequences, an (N+2)-dimensional matrix is needed to be filled with alignment scores.
6. In the method of extraction of blocks from a global or local MSA, a global MSA of related protein sequences usually includes regions that have been aligned without gaps in any of the sequences.
7. The major drawback of the progressive and iterative alignment strategies is that they are largely global alignment based and may therefore fail to recognize conserved domains and motifs among highly divergent sequences of varying lengths.
8. Which of the following is untrue about DIALIGN2?
9. Two considerations arise in trying to tune the PSSM so that it adequately represents the training sequences. Which of the following is not their description?
10. Although MOTIF program is used successfully for making the BLOCKS database, it is limited in the pattern sizes that can be found.
11. In EM algorithm, as an example, suppose that there are 10 DNA sequences having very little similarity with each other, each about 100 nucleotides long and thought to contain a binding site near the middle 20 residues, based on biochemical and genetic evidence. the following steps would be used by the EM algorithm to find the most probable location of the binding sites in each of the ______ sequences.
12. The substitution matrices are rarely used in this type of matching.
13. The quality and quantity of information provided by the PSSM also varies for ________ in the motif.
14. There is a unique advantage of multiple sequence alignment because it reveals more biological information than many pair wise alignments can.
15. Which of the following scores are not considered while calculating the SP scores?
16. Iterative methods include repeatedly realigning subgroups of the sequences and then by aligning these subgroups into a local alignment of all of the sequences.
17. In Genetic Algorithm, in the mutation process _______
18. The HMM is a statistical model that considers few combinations of matches and gaps to generate an alignment of a set of sequences.
19. Which of the following is not true regarding the BLOCKS?
20. Which of the following is not true regarding the BLOCKS?
21. Which of the following is untrue about Needleman-Wunsch algorithm?
22. There are two types matrices involved in the study- score matrices and trace matrices.
23. The pattern searching method type of analysis was performed on groups of related proteins, and the amino acid patterns that were located may be found in the Prosite catalog.
24. Which of the following is untrue about PRRN?
25. The global sequence alignment is suitable when the two sequences are of dissimilar length, with a negligible degree of similarity throughout.

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