Steinar Thorvaldsen

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Hidden Markov Models (HMM) can be extremely useful tools for the analysis of data from biological sequences, and provide a probabilistic model of protein families. Most reviews and general introductions follow the excellent tutorial by Rabiner, where the focus is outside biology. Mendel's famous experiments in plant hybridisation were published in 1866 and(More)
BACKGROUND Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, orthologous sequences from different habitats may be explored and compared. The main goal of the DeltaProt Toolbox is to provide users with(More)
The identification of specific amino acids (AAs) or groups of functionally important AA residues in ionizing radiation-resistant bacteria (IRRB) is an important challenge in understanding the biological basis of resistance to ionizing radiation (IR; X-rays and gamma-rays). To address this problem, we compared homologous sites in multiple alignments of(More)
Bio-sequences from ortholog proteins are well suited for statistical inference when the sequences can be divided into ordinal groups based on known environmental features or traits of the host organisms. In this paper two new regression models are described for extracting proteomic trends of extreme environments. The approach is based on physicochemical(More)
The periplasmic/extracellular bacterial enzyme endonuclease I was chosen as a model system to identify features that might be responsible for temperature- and salt adaptation. A statistical study of amino acid sequence properties belonging to endonuclease I enzymes from three mesophilic habitats (non-marine, brackish water and marine), and three marine(More)
Cold-adaptation strategies have been studied in multiple psychrophilic organisms, especially for psychrophilic enzymes. Decreased enzyme activity caused by low temperatures as well as a higher viscosity of the aqueous environment require certain adaptations to the metabolic machinery of the cell. In addition to this, low temperature has deleterious effects(More)
An inhomogeneous discrete Markov model is formulated for sexual random mating with diploid male and female individuals. The generations are nonoverlapping and of given sizes. The genetic variation is in a sexually neutral allele with two varieties, giving three different genotypes. Taking sex as a marker, the Markov model works with six genotypes. The sex(More)
Multiple sequence alignments can provide information for comparative analyses of proteins and protein populations. We present some statistical trend-tests that can be used when an aligned data set can be divided into two or more populations based on phenotypic traits such as preference of temperature, pH, salt concentration or pressure. The approach is(More)