Research on Optimization of DNA Restoration Algorithms Based on the Genetic Diagnosis and Words Reconstruction with Forbidden Words Under the Unit Shift Hypothesis

This paper is dedicated to DNA restoration approaches. The aim of the work is research on optimization of DNA restoration algorithms based on the genetic diagnosis and words reconstruction with forbidden words under the unit shift hypothesis. In this work we present methods of accuracy measurements for reconstruction algorithms, investigation on possibilities of optimization mentioned algorithms, propose approaches for optimize and measure the performance of each algorithm based on changes, test all algorithms on Genbank files and summarize possibilities of such DNA reconstruction methods, as well as give our thoughts on the most perspective combinations of DNA restoration algorithms and their optimizations in order to restore the DNA. The research is based on the text representation of DNA code. Methods of research are applied linguistics, development of a program for testing process, mathematical modelling and work with Genbank files. The paper contains 35 pages, 4 chapters, 17 illustrations, 5 schemes, 43 bibliography items, 2 appendices. Keywords: words reconstruction algorithms, reconstruction with forbidden words, genetic diagnosis, natural language processing, DNA reconstruction, shotgun sequencing, Euler cycles, de Bruijn mutligraphs, genome.