MASTERARBEIT - Fachhochschule Salzburg

InformationenVor- und Zuname: DI(FH) Roland J. GrafInstitution:Fachhochschule Salzburg GmbHStudiengang:Informationstechnik & System-ManagementTitel der Masterthesis: Multiples Sequenzalignment mit HiddenMarkov ModellenBetreuer an der FH: Univ. Doz. Dr. Stefan WegenkittlSchlagwörter1. Schlagwort: Multiple Sequence Alignment2. Schlagwort: Hidden Markov Model3. Schlagwort: Alignment ScoringAbstractThis thesis describes the development of a method for performing Multiple SequenceAlignments (MSAs) using Hidden Markov Models (HMMs).The developed solution implements a dynamic, iterative process for generating theMSA. After training the model using pre-aligned sequences (profile-MSA), sequencesare ranked and aligned with the model individually. The highest ranked sequences arethen merged with the profile-MSA, before an alternative algorithm (ClustalW) is usedto make partial improvements to the alignment. In a further step, the generated MSAis prepared such that it allows for an iterated profile-extension scheme much alike PSI-BLAST where new HMMs are generated on the basic of top scoring hits and theiralignments to the original MSA.The quality of alignments and the quality of progressive growing MSA is evaluated bygraphical and numerical comparisons. Both probability density functions of Z-scores aswell as the scattering of Z-scores are used to evaluate the discriminatory power of themodel. Finally shows the change of entropy, whether additional sequences increase theaverage information content of the emission matrix, and whether these changes affectthe results.iii