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Estatística
Título: A NOVEL APPROACH FOR DE BRUIJN GRAPH CONSTRUCTION IN DE NOVO GENOME FRAGMENT ASSEMBLY
Autor: ELVISMARY MOLINA DE ARMAS
Colaborador(es): SERGIO LIFSCHITZ - Orientador
Catalogação: 04/MAI/2020 Língua(s): ENGLISH - UNITED STATES
Tipo: TEXT Subtipo: THESIS
Notas: [pt] Todos os dados constantes dos documentos são de inteira responsabilidade de seus autores. Os dados utilizados nas descrições dos documentos estão em conformidade com os sistemas da administração da PUC-Rio.
[en] All data contained in the documents are the sole responsibility of the authors. The data used in the descriptions of the documents are in conformity with the systems of the administration of PUC-Rio.
Referência(s): [pt] https://www.maxwell.vrac.puc-rio.br/projetosEspeciais/ETDs/consultas/conteudo.php?strSecao=resultado&nrSeq=47791&idi=1
[en] https://www.maxwell.vrac.puc-rio.br/projetosEspeciais/ETDs/consultas/conteudo.php?strSecao=resultado&nrSeq=47791&idi=2
DOI: https://doi.org/10.17771/PUCRio.acad.47791
Resumo:
Fragment assembly is a current fundamental problem in bioinformatics. In the absence of a reference genome sequence that could guide the whole process, a de Bruijn Graph data structure has been considered to improve the computational processing. Notably, we need to count on a broad set of k-mers, biological sequences substrings. However, the construction of de Bruijn Graphs has a high computational cost, primarily due to main memory consumption. Some approaches use external memory processing to achieve feasibility. These solutions generate all k-mers with high redundancy, increasing the number of managed data and, consequently, the number of I/O operations. This thesis proposes a new approach for de Bruijn Graph construction that does not need to generate all k-mers. The solution enables to reduce computational requirements and execution feasibility, which is confirmed with the experimental results.
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