Proposta de uma nova abordagem para o processo de montagem de novo de sequências de DNA obtidas de sequenciadores de nova geração

• Ano de defesa: 2014
• Autor(a) principal: Couto, Adriano Donato
• Orientador(a): Cerqueira, Fábio Ribeiro
• Banca de defesa: Fietto, Juliana Lopes Rangel , Ferreira, Ricardo dos Santos
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: por
• Instituição de defesa: Universidade Federal de Viçosa
• Programa de Pós-Graduação: Mestrado em Ciência da Computação
• Departamento: Metodologias e técnicas da Computação; Sistemas de Computação
• País: BR
• Palavras-chave em Português: Bioinformática; Genômica; Sequenciamento de nucleotídeo; Teoria dos grafos
• Palavras-chave em Inglês: Bioinformatics; Genomics; Nucleotide sequencing; Graph theory
• Área do conhecimento CNPq: CNPQ::CIENCIAS EXATAS E DA TERRA::CIENCIA DA COMPUTACAO
• Link de acesso: http://locus.ufv.br/handle/123456789/2677

The study of genomes brought a lot of gains to Medicine, Pharmacology and many other important science fields. However, many challenges emerged as a consequence, specially in Computer Science. The big amount of data and its complexity to be analyzed make arduous to extract the information needed. As the DNA sequencers are not able to get the sequence of the whole molecule at a glance, the sequencing process breaks the molecule and works with a lot of fragments. Those fragments need to be assembled in a next step. In the new-generation sequencers, the sequen- cing process is much faster and cheaper, but they return much smaller fragments compared to the output from Sanger technology. Besides the bigger set of fragments, the interference of sequencing errors complicates the process, classified as NP-hard. To handle this problem, the current DNA fragment assemblers run a lot of pre and postprocesses in the amount of data, aiming to eliminate or at least reduce the common problems. In this work, we propose a new approach of maximum- weighted maximum matching (first proposed for data from Sanger sequencing) for k-mer graphs that returns simpler components to work with (called unipaths), fol- lowed by an heuristic to combine those new components. Therefore, we want to do the assembly process in fewer steps. This crossing works with elongation of paths by the combination of unipaths. With a score system, the assembler tries to get longer paths combining the shorter ones, while minimizing the use of repeated re- gions. Because this is the beginning of a new approach for short fragments, it was not our intention to achieve a complete DNA assembler at its first version, but only to validate the proposed concept. In this work, we give focus specifically on the xiiassembly of sequences from new-generation sequencers. During the experiments, we identified that the assembler was able to return satisfatory results for half of the samples, but it needs some adjustments to improve the other results. Those adjust- ments would solve specific problems that this tool does not address yet. We also found out that the coverage by reads is determinant factor to get good outputs from this assembler. There are some future works that are necessary, such as decreasing memory usage and running time, as well as comparing this tool with other current available solutions.