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Description:
An important research topic in bioinformatics is the analysis of DNA, the molecule that encodes the genetic information of all organisms. The basis for this is sequencing, a procedure in which the sequence of DNA bases is determined. In addition to the identification of variations in the base sequence itself, advances in sequencing methods and a steady reduction in sequencing costs open up new fields of research: the analysis of functionally relevant non-base-related changes, so-called epigenetics. An important example of such a mechanism is DNA methylation, a process in which methyl groups are added to DNA without altering the sequence itself. Methylation takes place only at specific sites, and the methylation information of human DNA consists of approximately 30 million methylation levels between 0 and 1 in total. This thesis deals with problems and solutions for each phase of DNA methylation analysis. The most advanced method for detecting DNA methylation based on resolution is Whole-Genome Bisulfite Sequencing (WGBS), a technique that modifies DNA at unmethylated sites. We describe the special in-silico treatment required to process this altered DNA and existing concepts as well as newly developed bioinformatic methods for efficient determination of DNA methylation levels and their further processing with our developed tool camel. A common downstream analysis step is the detection of differentially methylated regions (DMRs), for which we have implemented a modification of the widely used method BSmooth in order to deal with today’s common data sizes. Setting up and creating new sequencing protocols, e.g., the mentioned WGBS, is complicated and requires adjustments to several parameters. We have developed a method based on a linear program (LP) that can predict the duplicate rate of supersamples. This critical quality measure represents the proportion of redundant data that in most cases needs to be removed from any further analysis. By using our method, it becomes possible to test, adjust and improve ...