Bioinformatics Practice Test Questions: Sequence Alignment | Practice Test / Quiz / MCQs

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Bioinformatics Practice Test Questions: Sequence Alignment

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In bioinformatics, sequence alignment is a way of arranging DNA, RNA, or protein sequences to identify regions of similarity. These similarities may be a result of functional, structural, or evolutionary relationships between the sequences. Topics include: Protein Motifs and Domain Prediction, Motif and Domain Databases Using Regular Expressions, Motif and Domain Databases Using Statistical Models, Protein Family Databases, Global Sequence Alignment, Local Sequence Alignment, Motif Discovery in Unaligned Sequences, Dot Matrix Sequence Comparison, Dynamic Programming Algorithm for Sequence... Show more

In bioinformatics, sequence alignment is a way of arranging DNA, RNA, or protein sequences to identify regions of similarity. These similarities may be a result of functional, structural, or evolutionary relationships between the sequences.

Topics include: Protein Motifs and Domain Prediction, Motif and Domain Databases Using Regular Expressions, Motif and Domain Databases Using Statistical Models, Protein Family Databases, Global Sequence Alignment, Local Sequence Alignment, Motif Discovery in Unaligned Sequences, Dot Matrix Sequence Comparison, Dynamic Programming Algorithm for Sequence Alignment, Use of Scoring Matrices and Gap Penalties in Sequence Alignments, Assessing the Significance of Sequence Alignments, & Bayesian Statistics.

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Bioinformatics Practice Test Questions: Sequence Alignment

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1. Which of the following statements about PANTHER and TIGRFAMs databases is incorrect regarding its features?

PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertiseTIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotationTIGRFAMs provides a tool for identifying functionally related proteins based on sequence homologyHidden Markov models (HMMs) are not used in PANTHER

2. Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?

it is assumed that each amino acid position is not mutable at allit is assumed that each amino acid position is equally mutableit is assumed that each amino acid position is not equally mutablesites do not vary in their degree of mutability

3. Among the following which one is not the approach to the local alignment?

Words methodK-tuple methodNeedleman-Wunsch algorithmSmith-Waterman algorithm

4. Which of the following is not a disadvantage of Needleman-Wunsch algorithm?

This cannot be applied on genome sized sequencesThere is a need of intensive memoryThis method can be applied to even large sized sequencesThis method is comparatively slow

5. Which of the following doesn’t describe PAM matrices?

This family of matrices lists the likelihood of change from one amino acid to another in homologous protein sequences during evolutionThere is presently no other type of scoring matrix that is based on such sound evolutionary principles as are these matricesEven though they were originally based on a relatively small data set, the PAM matrices remain a useful tool for sequence alignmentIt stands for Percent Altered Mutation

6. Which of the following is false in case of the database SMART and its algorithm?

Alignments are further checked but not refined by human annotators before HMM profile constructionSMART stands for Simple Modular Architecture Research ToolAlignments in the database are built based on tertiary structures whenever available or based on PSI-BLAST profilesContains HMM profiles constructed from manually refined protein domain alignments

7. When random or unrelated sequences are compared using a global alignment method, they can have ____________ reflecting the tendency of the global algorithm to match as many characters as possible.

very high scoresmoderate scoresvery low scoreslow scores

8. Which of the following does not describe k-tuple methods?

They are useful in small scale databasesk-tuple methods are best known for their implementation in the database search tools FASTA and the BLAST familyThey are also known as words methodsThey are basically heuristic methods to find local alignment

9. What is the source of protein structures in SCOP and CATH?

EnsembleProtein Data BankInterProUniprot

10. Which of the following does not describe global alignment algorithm?

First row and first column are set to zeroIn initialization step, the first row and first column are subject to gap penaltyIn trace back step, beginning is with the cell at the lower right of the matrix and it ends at top left cellScore can be negative

11. A feature of the dynamic programming algorithm is that the alignments obtained depend on the choice of a scoring system for comparing character pairs and penalty scores for gaps.

Can't SayFalseTrueMaybe

12. _______ analyzed the distribution of scores among 100 vertebrate nucleic acid sequences and compared these scores with randomized sequences prepared in different ways.

Waterman, in 1987Lipman, in 1984Batalov, in 1964Lipman, in 1967

13. Which of the following statements about SUPERFAMILY database is incorrect regarding its features?

Sequences must be submitted in FASTA format onlyIt searches the database using a superfamily, family, or species name plus a sequence, SCOP, PDB or HMM ID’sIt has generated GO annotations for evolutionarily closed domains and distant domainsSequences can be submitted raw or FASTA format

14. On analysis of the alignment scores of random sequences will reveal that the scores follow a different distribution than the normal distribution called the _________

Gumbel equal value distributionGumbel distributionGumbel extreme value distributionGumbel end value distribution

15. The higher is the score in the alignment _________

the more significant is the alignmentthe less it aligns with the related protein sequencethe less significant is the alignmentor the less it resembles alignments in related proteins

16. After the derivation, the outputs of the dynamic programming are the ratios are called even scores.

MaybeTrueCan't SayFalse

17. Isolated dots that are not on the diagonal represent exact matches.

Can't SayMaybeFalseTrue

18. Which of the following is true for EMBOSS Dottup?

Doesn’t allow you to specify window sizeIf all cells in the window are identity, it colors in some specific cells in the windowAllows you to specify thresholdDoesn’t allow you to specify threshold

19. Which of the following does not describe global alignment algorithm?

For two sequences of length m and n, the matrix to be defined should be of dimensions m and nFor two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1It is based on dynamic programming techniqueScore can be negative in this method

20. When was this method, first described?

1970196619821959

21. A length and distance that gives the highest overall probability may then be determined. Such alignments are initially found using ________

dot methodan alignment algorithm and a particular scoring matrixan alignment algorithm onlya particular scoring matrix only

22. In Bayesian methods, difficulty with making estimations is that the estimate depends on the following Assumption. (Assumption – The mutation rate in sequences has been constant with time and that the rate of mutation of all nucleotides is the same.)

FalseMaybeTrueCan't Say

23. Which of the following statements about COG is incorrect regarding its features?

Currently, there are 4,873 clusters in the COG databases derived from unicellular organismsThe interface for sequence searching in the COG database is the COGnitor program, which is based on gapped BLASTIt is a protein family database based on structural classificationIt is constructed by comparing protein sequences encoded in forty-three completely sequenced genomes, which are mainly from prokaryotes, representing thirty major phylogenetic lineages

24. Which of the following does not describe local alignment?

A local alignment aligns a substring of the query sequence to a substring of the target sequenceThe substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also globalLocal alignments have terminal gapsA local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score

25. Point out the wrong or irrelevant mathematical method in motif analysis.

Deterministic OptimizationProbabilistic OptimizationEnumerationLiterature mining

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