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Analys av kovarianser i sekvensalignment
Analysis of sequence alignment covariances
Göbel et al developed an algorithm to mine sequence alignments for covariations between positions in the alignments in 1994. Subsequently Pazos et al developed an application of Göbel's algorithm to predict neighbouring pairs of amino acids in the interface between two interacting proteins. Inspired by these advances Dr Bergkvist started to design an alternative algorithm to satisfy the purpose of Göbel et al and Pazos et al. In contrast to the previous papers this algorithm is based on a statistical analysis of relevant biophysical properties of the amino acids in the sequence alignments. The result shows good promise. However, since the statistical analysis assumes no general previous interdependences of the protein sequences - evolutionary relationships between the sequences may give rise to artefacts in the analysis.
Specific plan and suitable previous knowledge:
The aim of the project is to continue to develop the algorithm by Dr Bergkvist. A compensation factor is necessary to take into account evolutionary relationships between the protein sequences and alleviate corresponding artefacts in the results. This compensation factor should be incorporated into the code. The algorithm has been developed in Java so far, but a transfer to C may be advantageous. In any case, the more advanced statistical analysis probably needs to be developed in C. Besides familiarity with these programming languages, experiences with any of the following may be advantageous: protein sequence alignment algorithms, phylogenetic relationships, DNA replication and repair, incorporation of genetic mutations, and evolution.
Göbel et al., Proteins: Structure, Function and Genetics 18 (1994), 309-317
Pazos et al., Journal of Molecular Biology 271 (1997), 511-523
Bioinformatics, Computer programming, Protein sequence alignments, Evolution, Phylogenetic relationships, Covariances, C, C++, Java, Statistics.
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