In the paper, the problem of isothermic DNA sequencing by hybridization, without any errors in its input data, is presented and an exact polynomial-time algorithm solving the problem is described. The correctness of the algorithm is con.rmed by an enumerative proof.
DNA sequencing remains one of the most important problems in molecular and computational biology. One of the methods used for this purpose is sequencing by hybridization. In this approach usually DNA chips composed of a full library of oligonucleotides of a given length are used, but in principle it is possible to use another types of chips. Isothermic DNA chips, being one of them, when used for sequencing may reduce hybridization error rate. However, it was not clear if a number of errors following from subsequence repetitions is also reduced in this case. In this paper a method for estimating resolving power of isothermic DNA chips is described which allows for a comparison of such chips and the classical ones. The analysis of the resolving power shows that the probability of sequencing errors caused by subsequence repetitions is greater in the case of isothermic chips in comparison to their classical counterparts of a similar cardinality. This result suggests that isothermic chips should be chosen carefully since in some cases they may not give better results than the classical ones.
In recent years, two developments revolutionized the molecular genetics. The first one is an enormously improved technique of the DNA sequencing. It is now possible to obtain in couple of hours and on the low cost, the full sequence of the human genome. The second one is the invention of the CRISPR-Cas technique, which allows the precise manipulations of genomes of living organisms. This technique was already successfully applied to “repair” human genes responsible for hereditary diseases. To some astonishment, applications of genetic engineering to humans does not bring protests of general public, while similar manipulations pf plants genomes are considered an dangerous. In Poland and in some other countries, parliaments introduced an extremely restrictive laws, which in practice makes cultivation of GM plants outside laboratories impossible. This is caused by the ignorance of the general public and by opposition of catholic church which considers genetic modifications of all organisms as contradictory with Gods will. The most common modification of plants is an introduction into their genomes of the single gene from the bacterium Bacillus thuringensis, what make the plant resistant to harmful insects. According to WHO, neither the manipulation mentioned above, nor manipulations of the other kind, do not pose any danger to humans.