## 2 The biological problems  
### The DNA  
A complete description of each living organism is represented by its _genome_. This can be thought of as a \"program\" in a special language, describing the set of instructions to be followed by the organism in order to grow and fully develop to its final form. The genome is a blueprint out of which each different form of life can be defined. The language used by nature to encode life is represented by the DNA code. A genome is made up by the deoxyribonucleic acid (DNA), present in each of the organism's cells, and consisting of two strands of tightly coiled threads of _nucleotides_, or _bases_. Four different bases are present in the DNA, namely adenine (A), thymine (T), cytosine (C) and guanine (G). The particular order of the bases, called the _genomic sequence_, specifies the precise genetic instructions to create a particular form of life with its own unique traits. The two DNA strands are inter-twisted in a typical helix form, and held together by weak bonds between the bases on each strand, forming the so called _base pairs_ (bp). A complementarity law relates one strand to its opposite, and the only admitted pairings are adenine with thymine (A \(\leftrightarrow\) T) and cytosine with guanine (C \(\leftrightarrow\) G). During cell division the DNA has the ability to replicate itself. In order to do so, the DNA molecule unwinds and the bonds between the base pairs break. Then, each strand directs the synthesis of a complementary new strand. The complementarity rules should ensure that the new genome is an exact copy of the old one. Although very reliable, this process is not completely error-free and some bases may be lost, duplicated or simply changed. Variations to the original content of a DNA sequence are known as _mutations_. In most cases mutations are deadly; in other cases they can be completely harmless, or lead, in the long run, to the evolution of a species. In humans the DNA in each cell contains about three billion base pairs. Human cells, as well as cells of most higher organisms, are _diploid_, i.e. their DNA is organized in pairs of _chromosomes_. The two chromosomes that form a pair are called homologous. Chromosomes come in pairs since one copy of each is inherited from the father and the other copy from the mother. While diploid cells have two copies of each chromosome, the cells of some lower organisms, such as fungi and single-celled algae, have only a single set of chromosomes. Cells of this type are called _haploid_. The process of reading out the ordered list of bases of a genomic region is called _sequencing_. Due to current technological limitations, it is impossible to sequence regions longer than a few hundred base pairs. In order to sequence longer regions, a preliminary step (DNA _amplification_) makes a large amount of copies of the target, which are then broken into small pieces at random. The pieces have then to be put together, to reconstruct the original sequence. In order to do so, the pieces are assembled and merged when they overlap for a sufficiently long part. The basic mechanism by which life is represented in nature is the same for all organisms. In fact, all the information describing an organism is encoded in its genome through DNA sequences, by means of a universal code, known as the _genetic code_. This code is used to describe how to build the _proteins_, which provide the structural components of cells and tissues, as well as the _enzymes_ needed for essential biochemical reactions. Not all of the DNA sequence contains coding information. As a matter of fact, only a small fraction does (in humans, roughly 10% of the total DNA is coding). The information-coding DNA regions are organized into _genes_, where each gene is responsible for the coding of a different protein. We can now define a first class of problems that are related with sequences, their classification, determination and management.