Multiple Choice Question - 12/Jun/2015

Regarding the paper "On the consecutive ones property" by Meidanis et al. (1998), and the algorithm that leads to the construction of PQR trees:

I - The algorithm is ONLINE
II - The overall running time of the algorithm is quadratic
III - The algorithm always constructs a PQR tree given a set and a collection (set of sets)

Which of the statements are correct?

a) Only I
b) Only II
c) Only III
d) Only II and III
e) None of the above

Original idea by: Gustavo Waku
Translation help by: Leandro Tacioli

Multiple Choice Question - 05/Jun/2015

According to the concept of equivalence transformations by Booth and Lueker (1976), which alternative DOES NOT represent a PQ-tree equivalent to the following tree?

a) 

b)

c)

d)

e) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 29/May/2015

Given the matrices below, which of the alternative represents matrices arranged in the "dictionary order" by Benzer (1959)?

a) Only I
b) Only I and IV
c) Only I, II and IV
d) Only II and IV
e) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 22/May/2015

In which of the following genomes is possible to sort using block interchanges?

a) +1 +5 +8 -2 +4 +3 -6 -7
b) -6 -1 -4 -2 -8 -3 -5 -7
c) +1 -2 -3 -4 -5 -6 -7 +8
d) +5 +4 +3 +1 -2 +6 +7 +8
e) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 15/May/2015

Considering the permutation (0, 5, 3, -1, -4, 2) and the concepts shown in Bergeron 2005, choose the WRONG alternative.

a) The oriented pair (0, -1) has score = 1 and the oriented pair (-1, 2) has score = 0
b) The resulting reduced permutation of the reversal induced by oriented pair (-1, 2) is (0, 3, 2, 1)
c) The permutation contains four oriented pairs: (0, -1), (5, -4), (3, -4) and (-1, 2)
d) The resulting reduced permutation of the reversal induced by oriented pair (-1, 2) is equal to the resulting reduced permutation of the reversal induced by oriented pair (-3, 4). The same operation occurs with oriented pairs (0, -1) and (5, -4).
e) None of the above

Original idea by: Ulisses Martins Dias
Translation help by: Leandro Tacioli

Multiple Choice Question - 08/May/2015 - Question 02

Considering the cycle of a linear chromosome as self-reverse-complementary, what is the chromosomal algebraic representation for the genome π?

a) π_chr = (A B -C X Y) (Z -D E) (-F W)
b) π_chr = (A B -C X Y Z -D E -F W)
c) π_chr = (-A -B C X Y -Y -X -C B A) (-Z D -E E -D Z) (F -W W -F)
d) π_chr = (-A -B C X Y -Y -X -C B A -Z D -E E -D Z F -W W -F)
e) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 08/May/2015 - Question 01

What is the main difference between the DCJ distance and the Algebraic distance formulas?

a) The DCJ distance formula considers only odd paths while the Algebraic distance formula considers only even paths
b) The DCJ distance formula considers only odd paths while the Algebraic distance formula considers all paths
c) The DCJ distance formula considers only even paths while the Algebraic distance formula considers only odd paths
d) The DCJ distance formula considers all paths while the Algebraic distance formula considers only odd paths
e) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 01/May/2015

How many orbits are created by the permutation between the two sets below?

a) 2
b) 4
c) 5
d) 8
e) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 24/Apr/2015

Which of the following evolution events can be modeled by one or more 'double-cut-and-join' (DCJ) operation applications?

I - Translocation
II - Reversal
III - Block interchange

1 - I and II
2 - I and III
4 - II and III
4 - I, II and III
5 - None of the above

Original idea by: João Paulo Pereira Zanetti
Translation help by: Leandro Tacioli

Multiple Choice Question - 17/Apr/2015

Considering the two liner genome below, what is the SCJ distance between them?

1) 5

2) 8

3) 10

4) 16

5) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 10/Apr/2015

Given the two fictious linear genome below, determine the set of adjacencies of the first genome that are different from the second.

1) { ND1_t ND2_t , ND4_t ATP_t }

2) { COX1_tCOX2_h, COX2_t ND3_t }

3) { ND1_hND2_t , ND2_hCOX1_h , ND3_hND4L_t , ND4L_hND4_t , ND4_hATP6_h }

4) { ND1_hND2_h , ND2_tCOX1_h , ND3_hND4L_h , ND4L_tND4_h , ND4_tATP6_t }

5) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 03/Apr/2015

Considering the matrix "Species vs. Characters" below, what is the number of changes necessary to create the most parsimonious tree?

1) 8
2) 10
3) 15
4) 18
5) None of the above

Original idea by: Leandro Tacioli

Multiple Choice Question - 27/Mar/2015

What is the main difference between the Kimura model and the Jukes-Cantor model?

1) The Kimura model is used only to study transitions, while the Jukes-Cantor model is used only to study transversions.
2) The Kimura model is a recursive representation of the Jukes-Cantor model.
3) The Kimura model has a better approach than the Jukes-Cantor model, because transitions and transversions receive different probabilities.
4) Both models are used to study different subjects, so there is no reason for comparisons.
5) None of the above

Original idea by: Douglas José Soares Rodrigues
Translation help by: Leandro Tacioli

Multiple Choice Question - 20/Mar/2015

Considering the Local Comparison method to compare two sequences, which of the following statements is FALSE?

1 - It uses the same matrix layout as global comparison
2 - The first row and the first column are initialized with zeros
4 - Empty prefixes always have zero value
4 - a[i,j] accepts negative values
5 - None of the above

Original idea by: Leandro Tacioli 

Multiple Choice Question - 06/Mar/2015

Which of these human cell structures contain genetic material (DNA)?

1 - Nucleus and Mitochondria
2 - Nucleolus and Ribosome
3 - Mitochondria and Chloroplast
4 - Nucleus and Chloroplast
5 - None of the Above

Original idea by: Leandro Tacioli

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