Submitted by Juliano Farias da Nobrega null (juliano@e8.com.br) on 2016-04-13T15:21:20Z No. of bitstreams: 1 dissert_juliano_unesp.pdf: 1652677 bytes, checksum: 2d05540d73450af0ce70d07689eeac2a (MD5) / Rejected by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br), reason: Solicitamos que realize uma nova submissão seguindo as orientações abaixo: O arquivo submetido está sem a ficha catalográfica. A versão submetida por você é considerada a versão final da dissertação/tese, portanto não poderá ocorrer qualquer alteração em seu conteúdo após a aprovação. Corrija esta informação e realize uma nova submissão contendo o arquivo correto. Agradecemos a compreensão. on 2016-04-14T20:43:40Z (GMT) / Submitted by Juliano Farias da Nobrega null (juliano@e8.com.br) on 2016-04-15T13:45:15Z No. of bitstreams: 1 Dissertacao_Juliano_Unesp.pdf: 1798501 bytes, checksum: 97b5fd5aa56bbac1dd28b2e73b516bd4 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-04-18T13:22:17Z (GMT) No. of bitstreams: 1 nobrega_jf_me_sjrp.pdf: 1798501 bytes, checksum: 97b5fd5aa56bbac1dd28b2e73b516bd4 (MD5) / Made available in DSpace on 2016-04-18T13:22:17Z (GMT). No. of bitstreams: 1 nobrega_jf_me_sjrp.pdf: 1798501 bytes, checksum: 97b5fd5aa56bbac1dd28b2e73b516bd4 (MD5) Previous issue date: 2016-02-29 / Recentemente, a bioinformática tornou-se um recurso imprescindível para a análise e interpretação da grande quantidade de informação biológica gerada pela biologia molecular e pelos sequenciadores de última geração. O processo de comparação dessas biossequências é o ponto de partida para o estudo da evolução e diferenciação dos organismos vivos, além de ser uma das tarefas mais importantes na biologia computacional. Neste trabalho apresenta-se uma abordagem baseada na heurística de Cadeias de Markov para otimização de um algoritmo de alinhamento múltiplo de sequências biológicas, proporcionando resultados com mais qualidade e sem o comprometimento do desempenho da ferramenta MUSCLE, escolhida para dar suporte ao trabalho. As cadeias de Markov foram escolhidas como técnica de otimização devido sua eficiente aplicabilidade em diversos problemas, sobretudo na biologia computacional, pois sua metodologia probabilística torna a aplicação computacionalmente viável, contornando os problemas NP-difícil e apresentando resultados significamente precisos. / Recently, bioinformatics has become an indispensable tool for analyzing and interpreting large amounts of information biological generated by molecular biology and the next-generation sequencers. The comparison process these sequences is the starting point for the study of evolution and differentiation of living organisms as well as being one of the most important tasks in computational biology. This work presents an approach based on Markov chains heuristics for optimization of a multiple alignment algorithm of biological sequences, provides improved quality results and without compromising the performance of MUSCLE tool chosen to support the work.. Markov chains were chosen as optimization technique due to its efficient applicability in various other problems, especially in computational biology, as its probabilistic methodology makes applying computationally feasible, bypassing the NP-hard problems and stating significantly accurate results.

Using bioinformatics we have identified stm3071 as a possible regulator of anaerobically induced genes involved in metal homeostasis (Price-Carter et al., 2001) and the aim of this study is to determine the function of stm3071 and define the conditions that induce its expression. Cobalt is required for incorporation into cobalamin (vitamin B12) which is important during S. Typhimurium infection. Vitamin B12 is synthesised de novo under anaerobic conditions and is required for metabolism of 1,2-propanediol and ethanolamine which act as sources of carbon and nitrogen when Salmonella is in the gut (Raux et al., 1996; Thiennimitr et al., 2011). Therefore, sensing Co2+ from the environment, and maintaining Co2+ homeostasis, to avoid metal-mediated toxicity, is required for vitamin B12 biosynthesis. Using λ-red based mutagenesis we have constructed a deletion mutant in order to investigate the function of stm3071. We examined the effect of mutation on the utilisation of 1,2-propanediol under anaerobic conditions and ability to produce vitamin B12. We have also tested the effect of mutation on tolerance to cobalt both aerobically and anaerobically. In order to monitor conditions in which Pstm3071 is switched on, a Pstm3071::lacZ transcriptional fusion was constructed in plasmid pRS415. Levels of β-galactosidase activity were measured in the presence of cobalt in both Δstm3071 and SL1344 (wild type strain) under anaerobic conditions. Anaerobic growth experiments and B12 assays showed that stm3071 is not essential for growth or synthesis of vitamin B12. In addition, cobalt tolerance in both aerobic and anaerobic conditions was unaffected. However, as measured by β-galactosidase assay, our data suggests that Pstm3071 expression is induced in the presence of cobalt in the deletion mutant. In contrast, we observed no difference in expression of Pstm3071 in the presence or absence of cobalt in SL1344.

Gene detection in DNA sequences is one of the most difficult problems, which have been currently solved in bioinformatics. This thesis deals with gene detection in DNA sequences with methods using Hidden Markov Models. It contains a brief description of the fundamental principles of molecular biology, explains how genetic information is stored in DNA sequences, as well as the theoretical basis of the Hidden Markov Models. Further is described subsequent approach in the design of specific Hidden Markov Models for solving the problem of gene detection in DNA sequences. Is designed and implemented application, which uses previously designed Hidden Markov model for gene detection. This application is tested on the real data, results of these tests are discussed in the end of the thesis, as well as the possible extension and continuation of the project.