A statistical score for assessing the quality of multiple sequence alignments

v2006okBEL/MG

Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.Siirretty Doriast

The Phylogenetic Analysis Of Genes Encoding Specific Steps In The Glutathione Pathway Within Industrial Beer Brewing Strains: Saccharomyces Cerevisiae, Saccharomyces Pastorinus, And The Spoilage Microbe Brettanomyces

The Glutathione pathway, (GSH) is an antioxidant system in yeast that increases cell viability and contributes to the production of desirable beer flavors during industrial fermentation. Despite its importance, studies using the GSH pathway: GSH1, GSH2, GLR1, and SOD1 genes, to trace the evolutionary history of beer strains are lacking. As a result, the investigator sought to elucidate the phylogenetic relationships between four commonly used industrial beer strains: California Ale, London Ale, Oktoberfest, and Brettanomyces bruxellensis through single-gene sequencing analysis of the GSH pathway. It was hypothesized that the actions of these GSH genes are unique and potentially upregulated in beer brewing yeasts when compared to non-brewing yeasts strains. In order to assess this theory, GSH pathway genes from the experimental industrial strains, were sequenced in order to demonstrate that brewing yeast exhibit identical GSH pathway sequences as an adaptation to their shared brewing environments. Following genome sequencing and phylogenetic analyses, the investigator found that these strains possessed identical GSH pathways as a result of various physiological adaptations and prolonged use within industrial settings. The investigator’s results highlight the evolutionary significance and functionality of GSH pathway genes and demonstrate the essentialness of antioxidant activity in industrial yeast strains. These results also revealed that important strain related associations can be inferred through an analysis of essential metabolic pathways

Statistical methods for conservation and alignment quality in proteins

v2008okDiss.: Turun yliopisto, 200

A tool for assessing the quality of multiple sequence alignments

Tato bakalářská práce se zabývá testováním kvality vícenásobného zarovnání biologických sekvencí. Obsahuje literární rešerši veřejně dostupných nástrojů vícenásobného zarovnání. Stěžejní bod práce tkví v programu pro testování kvality vícenásobného zarovnání (vytvořené pomocí různých nástrojů, při odlišném nastavení, aj.). Program má uživatelské rozhraní vytvořené v Matlabu a je k práci přiložen společně se souborem nukleotidových a proteinových sekvencí, sestavených za účelem testování a aplikování programu. V neposlední řadě je v práci obsaženo hodnocení veřejně dostupných nástrojů vytvořené na základě výpočtů programu.This thesis is dealing with quality assessment of multiple sequence alignments. It contains literature review of public available tools of multiple sequence alignments. The main part of this thesis focuses on the program on quality assessment of multiple sequence alignments (created with the help of various tools, using different settings, etc.). The program has a graphical user interface created in Matlab and is enclosed together with a set of nucleotide and protein sequences compiled for program testing and aplication. Last but not least, the thesis contains the assessment of public available tools resulting from program outputs.

Multigene datasets for deep phylogeny

Though molecular phylogenetics has been very successful in reconstructing the evolutionary history of species, some phylogenies, particularly those involving ancient events, have proven difficult to resolve. One approach to improving the resolution of deep phylogenies is to increase the amount of data by including multiple genes assembled from public sequence databases. Using modern phylogenetic methods and abundant computing power, the vast amount of sequence data available in public databases can be brought to bear on difficult phylogenetic problems. In this thesis I outline the motivation for assembling large multigene datasets and lay out the obstacles associated with doing so. I discuss the various methods by which these obstacles can be overcome and describe a bioinformatics solution, TaxMan, that can be used to rapidly assemble very large datasets of aligned genes in a largely automated fashion. I also explain the design and features of TaxMan from a biological standpoint and present the results of benchmarking studies. I illustrate the use of TaxMan to assemble large multigene datasets for two groups of taxa – the subphylum Chelicerata and the superphylum Lophotrochozoa. Chelicerata is a diverse group of arthropods with an uncertain phylogeny. When a set of mitochondrial genes is used to analyse the relationships between the chelicerate orders, the conclusions are highly dependent upon the evolutionary model used and are affected by the presence of systematic compsitional bias in mitochondrial genomes. Lophotrochozoa is a recently-proposed group of protostome phyla. A number of distinct phylogenetic hypotheses concerning the relationships between lophotrochozoan phyla have been proposed. I compare the phylogenetic conclusions given by analysis of nuclear and mitochondrial protein-coding and rRNA genes to evaluate support for some of these hypotheses

Alinhamento estratégico e operacional em relação ao marketing mix: um estudo na cadeia produtiva do café da região Sul de Minas - Brasil.

Doutoramento em GestãoDiante da importância apresentada pelos estudos desenvolvidos sobre o alinhamento em cadeias de suprimento, bem como dos atributos do marketing mix, esta investigação estabeleceu como objetivo verificar se ações de produtores e gestores da indústria de torrefação e moagem, na cadeia de suprimentos do agronegócio do café verde, da Região Sul de Minas, estão alinhadas, estratégica e operacionalmente, em relação aos atributos do marketing mix, mais concretamente em relação a produto, preço, promoção e sistema de distribuição. Especificamente, visa entender as estratégias de distribuição dos produtores de café verde, dos seus clientes (indústria de torrefação e moagem) e analisar o alinhamento entre as ações por eles adotadas. A hipótese central é a de que não existe alinhamento estratégico e operacional entre as ações por eles adotadas. Utilizou-se metodologia não participante, do tipo survey, tendo como objeto de estudo a cadeia de suprimento do café, da Região Sul de Minas, Brasil. Adotou-se a orientação de Chopra e Meindl, que consiste primeiro em entender o cliente ou o mercado, depois, perceber a cadeia de suprimentos e, finalmente, verificar o alinhamento entre cliente e cadeia de suprimentos. Os resultados encontrados mostraram a existência de várias ações semelhantes e outras diferentes. Desta forma, concluiu-se que parte significativa das ações de produtores e gestores da indústria de torrefação e moagem de café verde, na região Sul de Minas, está alinhada quanto aos atributos do marketing mix, enquanto outras não. Dessa forma, rejeita-se a hipótese para uma parte significativa dos atributos analisados e aceita-se esta hipótese para outra parte desses atributos.Given the importance attributed by the studies conducted on the alignment in supply chains, as well as the attributes of the marketing mix, this investigation aims to study the strategic and operational alignment between actions of producers and industry managers of roasting and grinding green coffee relatively the attributes of the marketing mix, specifically in relation to product, price, promotion and distribution system. We seek specifically to understand the strategies of distribution of green coffee producers, their customers (industry of roasting and grinding) and to analyze the alignment between their actions. The central hypothesis is that there is alignment between the strategic and operational actions. The methodology focus on a non-participant survey type, having as object of study the supply chain of coffee, in the Southern Region of Minas Gerais, Brazil. We adopted the model from Chopra and Meindl, which consists first in understanding the customer or the market, then in realizing the supply chain and, finally, checking the alignment between client and supply chain. The results showed the existence of several similar actions and other that are different. Thus, we came to the conclusion that a significant portion of the shares of producers and industry managers of roasting and grinding green coffee, in the South of Minas, is aligned as attributes of th e marketing mix, while others are not. Therefore, we reject the hypothesis for a significant part of the attributes analyzed and accepted it concerning another part.N/