Week 15 (PQR-Tree)

Choose the WRONG alternative regarding PQ-Tree and PQR-Tree:

a) Every PQ-Tree is an PQR-Tree, but the reverse isn't valid.
b) The children of an R node can permute without any rule between them and the same occurs in the Q node.
c) Intersection, disjoint union and complement not contained are operations that can be used to calculate the completion of set.
d) There always is a PQR-Tree that represents an set of restrictions, independent of this set.
e) None of Above.

Original idea by: Celmar Guimarães da Silva
Translation help by: Andrey Victor Justo

Week 14 (PQ-Tree)

Given the alternatives below, choose the INCORRECT statement:

a ) To get the FRONTIER(T) of a tree, you just read all the leaves from left to right.
b ) The null tree isn't an PQ-Tree
c ) Reverse a P-node is a equivalent transformation.
d ) Reverse a Q-node is a equivalent transformation.
e) None of above.

Original idea by: Moacy Barros Correia da Silva
Translation help by: Andrey Victor Justo

Week 13 (Genetic fine structure)

Following the text "On the topology of the genetic fine structure", consider the statements blow:

I - The recombination test verify if given two mutants is possible to generate again the original gene.

II - The recombination test is an experiment that is essentially quantitative.

III - The matrix of recombination shows that two mutants can generate again the original linear structure; and when reordered in the dictionary order has an feature that is semiotic matrix and for any column or row, starting in the diagonal to the right or down the sequence of zeros form a continuos block, unbroken by one.

IV - Choosen mutants in the article are non-reversible and can have until two separated modifications by which block without modification.

Which the statements above are correct?

a) Only I and II.

b) Only I and III.

c) Only II and IV.

d) Only II, III and IV.

e) None of above

Original Idea by: Gustavo Waku
Translated by: Andrey Victor Justo

Week 12 (Unichromosomal reversal distance, Hannenhalli and Pezvner 1999, Bergeron 2005)

Following the article by Anne Bergeron, A Very Elementary Presentation Of Hannenhalli-Pevzner Theory, 2006, which of the alternatives don`t represent the minimal score reversal of p = (1 -5 2 4 -3 -8 7) ?

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

Original Idea by: Adriano Batista Prieto
Translated by: Andrey Victor Justo

Week 11 (Matrix Medians and Unichromossomal reversal distance)

According to the Anne Bergeron text, choose the right answer below:

a) An oriented pair (πi, πj), i < j, is a pair with consecutive integers with the same signal.
b) An induced reversal given by an oriented pair (πi, πj) is ρ(i + 1,j - 1). 
c) A hurdle is a framed interval which doesn't have any other smaller framed interval inside it.
d) One super-hurdle is a hurdle which can't be cut.
e) None of above.

Original idea by: Luis Felipe Strano Moraes
Translation help by: Andrey Victor Justo

Week 9 (Permutation)

Consider the following permutation below and choose the right answer:

a) The support of this permutation is {4,5,6}.
b) The breakdown of this permutation in disjointed cycles in pairs produce exactly three cycles with lenght greater than 1.
c) The permutation is one 6-cycle.
d) The breakdown of this permutation in disjointed cycles in pairs can be represented by: (173)(298).
e) None of above.

Original idea by: José Augusto Amgarten Quitzau
Translation help by: Andrey Victor Justo

Week 8 (Double-Cut-and-Join)

In the genome rearrangement there always is a DCJ operation which reduce the difference between the number of breakpoints and the number of cycles by one unit, except when the genome have been ordered. Others features of this problem are:

a) The DCJ operation can't increase (b - c).
b) The DCJ operation always increase the number of cycles.
c) The DCJ operation always reduce the number of breakpoints.
d) The genomic distance, considering the DCJ operation, is equal of (b - c).
e) None of above.

Original idea by: Fabio L. Usberti
Translation help by: Andrey Victor Justo

Week 7 (Single-Cut-or-Join)

Consider the statements below and choose the right answer about SCJ:

I - SCJ is a new way to compute the distance between two genomes that can be used to solve the MGRP (multiple genome rearrangement problem).
II - SCJ is NP-hard.
III - For SCJ problem have been provided linear and polinomial time algoritms.


a) I.
b) I and III.
c) II
d) I and II.
e) None of Above.


Original idea by: Andrey Victor Justo

Week 6 (Genome Rearreagements)

Choose the WRONG alternative about genome rearreagements:

a) Rearreagements events represents the changing of segments of the genome.
b) Segments of the genome can be exchanged between the strips of the DNA.
c) There isn't a rearreagement event that change the number of genes in the genome.
d) The genome can be broke in two or more smaller genomes.
e) None of Above.

Original idea by: Leonardo Elias Mariote
Translation help by: Andrey Victor Justo

Week 5 (Phylogeny Problems)

The Parsimony methods have been used to build phylogenic trees and they have one of the objectives below:

a) Search for a phylogeny that has the lowest number of outgroups among the species analyzed.
b) Search for a phylogeny that has the greatest possible number of species in the tree leaves, i.e., species that aren't ancestors.
c) Search for phylogenetic tree that does't have a root.
d) Search phylogeny that has the lowest possible number of homoplasies.
e) None of above.

Original idea by: Mirela Dal Col Silva
Translation help by: Andrey Victor Justo

Week 4 (DNA Evolution Models)

Given models of sequence evolution of Jukes-Cantor and Kimura, choose the right option:

a) The two parameters of model Kimura doesn't consider differential rates of mutations between same family of nucleotides.
b) In the molecular evolution of the number of transitions tends to be larger than the number of transversions.
c) The main difference introduced by Kimura was treating different frequencies bases.
d) The distance between two sequences, when measured using the model of Kimura and Jukes-Cantor tends to be very different even between almost identical sequences.
e) None of above.

Original idea by: Luis Felipe Strano Moraes
Translation help by: Andrey Victor Justo

Thinking about computational data structures, which one of the structure below is the best to save a gene given by a human characteristic?

a) Linked-List

b) HashMap

c) Binary Tree

d) k-d Tree

e) None of above

Original idea by: Andrey Victor Justo