PUB - Publikationen an der Universität Bielefeld

Part I: Algorithmic Support for the PCR. Who would have thought a bacterium living in a hot spring in Yellowstone National Park would spark a revolutionary new laboratory technique? The polymerase chain reaction, now widely used in research laboratories and doctor's offices, relies on the ability of DNA-copying enzymes to remain stable at high temperatures. No problem for Thermus aquaticus, the sultry bacterium from Yellowstone that now helps scientists produce millions of copies of a single DNA segment in a matter of hours. The success of a PCR experiment also crucially depends on a pair of primers - short oligonucleotides that hybridize to selected templates on complementary strands of the target DNA. Our biocomputing software GeneFisher offers novel functionality like improved protein to DNA backtranslation, a more exact melting temperature calculation and the astounding concept of Single Primer PCR, which is based on the detection of unique, palindromic DNA template regions. This improved version of GeneFisher extends the efficiency of primer design significantly. This thesis seems to cover two areas of work which, at the first glance, appear quite unrelated. However, there is a strong connection: The idea of single primer PCR, that arose within Part I, required matching palindromic patterns, a subcase of approximate repeat analysis. Only after completion of the work presented in Part II, single primer PCR could become reality. Part II: Large Scale Genome Analysis. The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The GenAlyzer program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance, interactive visualization, and simple interfacing to other analysis programs.