O problema da ordenação de permutações usando rearranjos de prefixos e sufixos

Author(s)

Carla Negri Lintzmayer

• Document type: Doctoral Thesis
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Computação
• Defense date: 2016-12-15

Examining board members

Zanoni Dias; Maria Emilia Machado Telles Walter; Cristina Gomes Fernandes; Eduardo Candido Xavier; Fábio Luiz Usberti

• Advisor: Zanoni Dias

Abstract

The goal of the Pancake Flipping problem is to sort a stack of pancakes that have different sizes by performing as few operations as possible. The operation allowed is called prefix reversal and, when applied, flips the top of the stack of pancakes. Such problem is an interesting combinatorial problem by itself, but it has some applications in computational biology. Given two genomes that share the same genes and assuming that each gene appears only once per genome, we can represent them as permutations (stacks of pancakes are also represented by permutations). Then, we can compare the genomes by figuring out how one was transformed into the other through the application of genome rearrangements, which are large scale mutations. Reversals and transpositions are the most commonly studied types of genome rearrangements and a prefix reversal (or prefix transposition) is a type of reversal (or transposition) which is restricted to the beginning of the permutation. When the rearrangement is restricted to the end of the permutation, we say it is a suffix rearrangement. A problem of sorting permutations by rearrangements is, therefore, the problem to find a sequence of rearrangements with minimum cost that sorts a given permutation. The traditional approach considers that all rearrangements have the same unitary cost, in which case the goal is trying to find the minimum number of rearrangements that are needed to sort the permutation. Numerous efforts have been made over the past years regarding this approach. On the other hand, a long rearrangement (which is in fact a mutation) is more likely to disturb the organism. Therefore, weights based on the length of the segment involved may have an important role in the evolutionary process. We say this is the length-weighted approach and the goal is trying to find a sequence of rearrangements whose total cost (the sum of the cost of each rearrangement, which depends on its length) is minimum. In this thesis we present the first results regarding problems of sorting permutations by prefix and suffix reversals and transpositions considering both the traditional and the length-weighted approach. For the traditional approach, we considered a total of 10 problems and developed new results for 6 of them. For the length-weighted approach, we considered a total of 13 problems and developed new results for all of them (AU)

• FAPESP's process: 13/01172-0 - The sorting permutations problem using prefix and suffix operations
• Grantee: Carla Negri Lintzmayer
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)