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Metaheuristics for String Problems in Bio-informatics by Paola Festa, Christian Blum

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1Introduction

In computer science, a string s is defined as a finite sequence of characters from a finite alphabet Σ. Apart from the alphabet, an important characteristic of a string s is its length which, in this book, will be denoted by |s|. A string is, generally, understood to be a data type i.e. a string is used to represent and store information. For example, words in a specific language are stored in a computer as strings. Even the entire text may be stored by means of strings. Apart from fields such as information and text processing, strings arise in the field of bioinformatics. This is because most of the genetic instructions involved in the growth, development, functioning and reproduction of living organisms are stored in a molecule which is known as deoxyribonucleic acid (DNA) which can be represented in the form of a string in the following way. DNA is a nucleic acid that consists of two biopolymer strands forming a double helix (see Figure 1.1). The two strands of DNA are called polynucleotides as they are composed of simpler elements called nucleotides. Each nucleotide consists of a nitrogen-containing nucleobase as well as deoxyribose and a phosphate group. The four different nucleobases of DNA are cytosine (C), guanine (G), adenine (A) and thymine (T). Each DNA strand is a sequence of nucleotides that are joined to one another by covalent bonds between the sugar of one nucleotide and the phosphate of the next. This results in an alternating sugar–phosphate ...

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