With respect to PQ and PQR trees, select the incorrect alternative:

     a) All PQ tree is a PQR tree, but the opposite is not valid.
     b) The children of a node R can arbitrarily permutate with each other, as well as the children of a node Q.
     c) Intersection, disjoint union and noncontained complement are operations used to calculate the completion of a collection of sets.
     d) There is always a PQR tree that represents a collection of sets, regardless of what is this set.
     e) None of the above.

Original idea by: Celmar Guimarães da Silva
Translate help: Leandro José de Bortoli

In a PQ-tree, with respect to a new restriction, which of the following statements is true?

   a. If a node is partial, then none of its child nodes is full
   b. If a node is partial, then none of its child nodes is pertinent
   c. If a node has any of its child nodes empty, then it can only be an empty node
   d. If a node has any of its child nodes full, then it can only be a pertinent node
   e. None of the above

Original idea by: Priscila Nascimento Biller
Translate help by: Leandro José de Bortoli

Given the genome {1 8 3 9 7 6 2 5 4}, what is the block exchange distance defined by Christie (1996)?

1. 3
2. 4
3. 5
4. 6
5. None of the above.

Original idea by: Leandro José de Bortoli

According to the article by Anne Bergeron, A Very Presentation Elementary Theory of Hannenhalli-Pevzner, 2005, which of the alternatives below DON'T represents the result of a reversal which minimizes the resulting score when applied at p = (1 6 4 -3 -5 2 7 -8)? 

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

Original idea by: Adriano Batista Prieto
Translate help by: Leandro José de Bortoli

What is the result of applying the signed reversal ρ (B, D) in the circular genome π = (ABCD) (D -B -C -A)?

1. ρπ = (B C -A -D) (D A -C -B)
2. ρπ = (A B C D) (-D -C -B -A)
3. ρπ = (B C -D -A) (-C -B A D)
4. ρπ = (-D -C -B A) (-A B C D)
5. None of the above.

Original idea by: Marcus Vinícius Benedito
Translate help: Leandro José de bortoli

Which of the evolution events can be modeled by one or more double-cut-and-join operations?

I - Translocation
II - Reversion
III - Block Exchange

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

Original idea by: João Paulo Pereira Zanetti
Translate help: Leandro José de Bortoli

Given the sequence π = (-3, 2, -5, -6, 7, -8, 1, 4, 9), which of the following sequences can be obtained from π by applying a reversal?

1. (-3 -7 6 5 -2 -8 1 4 9)
2. (9 4 1 -8 7 -6 -5 2 -3)
3. (3 -2 5 6 -7 8 -1 -4 -9)
4. (-3 -2 -5 -6 -7 -8 1 4 9)
5. NDA

Original Idea by: Danilo Brandão Gonçalves
Translate help: Leandro José de Bortoli

Given the data set and tree below, using the parismony method choose the right answer.

1. The minimun changes of state needed is 7.
2. The minimun changes of state needed is 8.
3. The reconstruction of the character 2 has two change of states.
4. The reconstruction of the character 3 has two change of states.
5. None of the above.

Original Idea by: Leandro José de Bortoli

Regarding the evolution models studied in class., we can say that:

1. The Jukes-Cantor model is further refined, it ignores "transitions" less common in nature considering only the "transversions", which are more common mutations.
2. Kimura model is inefficient because it has only two parameters, one for the probability of a mutation occurs, and one for the probability of the position remain unchanged.
3. The Jukes-Cantor model is more refined than the Kimura model because it take into consideration the different mutation rates along the length of the sequence.
4. Kimura model is more refined than the Jukes-Cantor by taking into account the difference that normally exists between the rate of change of type "transversion" and the rate of change of type "transition".
5. NDA

Original idea by: José Augusto Amgarten Quitzau
Translate Help: Leandro José de Bortoli

Which of the following modifications do not need to be made to transform the global alignment algorithm in the local alignment algorithm?

1. Initialize with zero the first column and the first row of the matrix.
2. Stop the reconstruction of a local alignment when it finds an 0 in the matrix.
3. Do not let the matrix values become negative; if the maximum value is negative, should be replaced by 0.
4. Find the highest value of the entire matrix to obtain the similarity and to use as a starting point for reconstruction of an optimal alignment.
5. None of the above.

Original idea by: Filipe Benevides Netto
Translation help by: Leandro José de Bortoli. 

Regarding problem classes, we can say that:

1. NP problems can not be solved in polynomial time.
2. Any NP problem can be reduced in polynomial time to an NP-complete problem. 
3. There is an intersection between the classes P and NP, which does not completely includes none of the two.
4. The classes P and NP  are proven differently.
5. None of the above.

Original idea by: Tiago Rinck Caveden.
Translation help by: Leandro José de Bortoli.

Question 1

Regarding protein synthesis, it is true that:

a) translation is the process of copying genes into mRNAs molecules.
b) exons are the ends codons of a gene.
c) tRNAs carry amino acids to the ribosome.
d) All organisms have the same genetic code.
e) NDA

Author: Leandro José de Bortoli