Bioinformatics Online Test

1. Waterman, in1989, provided a set of means and standard deviations of global alignment scores between random DNA sequences, using mismatch and gap penalties that produce a linear increase in score with _______ a distinguishing feature of global alignments.

2. Which of the following is incorrect about Phrap?

3. Which of the following is untrue regarding Prediction with Neural Networks?

4. MEME stands for _____________

5. Which of the following is a wrong statement?

6. In the program DIALIGN, pairs of sequences are aligned to locate aligned regions that do not include gaps, much like continuous diagonals in a dot matrix plot.

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

8. Even if many pseudocounts are added in comparison to real sequence counts, the amino acid frequencies will not have any effect or influence.

9. To obtain a species phylogeny, phylogenetic trees from a variety of gene families need to be constructed.

10. The quality and quantity of information provided by the PSSM also varies for ________ in the motif.

11. Which of the following is untrue regarding Ab Initio–Based Methods?

12. Rosetta is a web server that predicts protein three-dimensional conformations using the ab initio method.

13. Which of the following is an incorrect statement about Newick Format?

14. Which of the following is incorrect regarding 2D-Page?

15. The databases Genbank, EMBL and DDBJ are updated daily.

16. Due to the requirement for co-regulation as well as colocalization, the method is mostly limited to certain classes of protein-protein interactions.

17. Telomeres hold newly replicated daughter chromosomes together.

18. In predicting RNA secondary structure, some simplifying assumptions are usually made, like the _____ structure is similar to the _____

19. The more conserved amino acids in similar proteins from different species are ones that play an essential role in structure and function and the less conserved are in sites that can vary without having a significant effect on function.

20. Which of the given statement is incorrect?

21. If the random sequences were prepared in a way that maintained the local base composition by producing them from overlapping fragments of sequence, the distribution of scores has a _______ standard deviation that is closer to the distribution of the natural sequences.

22. Which of the following does not describe PAM matrices?

23. Which of the following is untrue regarding the block analysis method?

24. The use of low-complexity masking in the BLAST procedure means that it may have higher specificity than FASTA because potential false positives are reduced.

25. The justification behind Rosetta stone method is that when two domains are fused in a single protein, they have to be in _______ proximity to perform a common function.

26. In the Interaction map of domain families, the interactions of one family represent the sum of all the interactions of domains in that family.

27. _____ of the human genome comprises one particular family of the SINE Element, designated Alu (1.2 million copies).

28. Which of the following is untrue regarding Prediction with Neural Networks?

29. In which of the following multipurpose packages Gibbs sampling algorithm is used?

30. The HMM is a statistical model that considers few combinations of matches and gaps to generate an alignment of a set of sequences.

31. In addition to the RNA polymerase, there are also a number of DNA-binding proteins that facilitate the process of transcription.

32. Which of the given statement is incorrect about proteome analyses?

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

34. The burial of surface area (or the maximization of surface contact) is an approximation of the effect of shape complementarity.

35. In the analysis of microarray data--If replicated datasets are available, rigorous statistical tests such as t-test and analysis of variance (ANOVA) can be performed to test the null hypothesis that a given data point is not significantly different from the mean of the data distribution.

36. Physical maps are maps of locations of identifiable landmarks on a genomic DNA _______ inheritance patterns.

37. The specificity refers to the ability to include incorrect hits.

38. The GOR method is based on the “propensity” of each residue to be in one of the two conformational states, helix (H), strand(E).

39. Like Mfold, RNAfold only examines the energy terms of the optimal alignment in a dot plot.

40. Which of the following is untrue regarding expressed sequence tags (ESTs)?

41. Which of the following is untrue about PredictionUsing NeuralNetworks for Gene Prediction?

42. Which of the following is untrue regarding the classic yeast two-hybrid method?

43. In dot matrix in ab initio methods, one way to reduce the noise in the matrix is to select an appropriate window size of a maximum number of contiguous base matches.

44. Which of the given is wrongly matched?

45. The specific DNA sequences to which the transcription factors bind are referred to as _____

46. The retroposons include short _________ interspersed nuclear elements (SINES).

47. which of the given statements is incorrect about Block multiple sequence alignment format?

48. A common recommendation is to use at least two of the methods—maximum parsimony, distance, or maximum likelihood, for the analysis.

49. In bacteria, the majority of genes have a start codon ATG (orAUG in mRNA; because prediction is done at the DNA level, T is used in place of U), which codes for methionine.

50. Once an operon structure is known ______ for the presence of a promoter and regulatory elements _____ in the operon do not possess such DNA elements.