Introduction: Bioinformatics is a promising young field that applies computer technology in molecular biology and develops algorithms and methods to manage and analyze biological data. Because DNA and protein sequences are essential biological data and exist in huge volumes as well, it is important to develop effective methods to compare and align biological sequences and discover bio sequence patterns.
Before we get into further details, let’s look at the type of data being analyzed. DNA and proteins sequences are long linear chains of chemical components. In the case of DNA, these components or “building blocks” are four nucleotides (also called bases), namely adenine (A), cytosine (C), guanine (G), and thymine (T). In the case of proteins, the components are 20 amino acids, denoted by 20 different letters of the alphabet. A gene is a sequence of typically hundreds of individual nucleotides arranged in a particular order. A genome is the complete set of genes of an organism. When proteins are needed, the corresponding genes are transcribed into RNA. RNA is a chain of nucleotides. DNA directs the synthesis of a variety of RNA molecules, each with a unique role in cellular function.
The alignment is based on the fact that all living organisms are related by evolution. This implies that the nucleotide (DNA, RNA) and proteins sequences of the species that are closer to each other in evolution should exhibit more similarities. An alignment is the process of lining up sequences to achieve a maximal level of identity, which also expresses the degree of similarity between sequences. Two sequences are homologous if they share a common ancestor. The degree of similarity obtained by sequence alignment can be useful in determining the possibility of homology between two sequences. Such an alignment also helps determine the relative positions of multiple species in an evolution tree, which is called a phylogenetic tree. This is followed by methods for multiple sequence alignment. Before we get into further details, let’s look at the type of data being analyzed. DNA and proteins sequences are long linear chains of chemical components. In the case of DNA, these components or “building blocks” are four nucleotides (also called bases), namely adenine (A), cytosine (C), guanine (G), and thymine (T). In the case of proteins, the components are 20 amino acids, denoted by 20 different letters of the alphabet. A gene is a sequence of typically hundreds of individual nucleotides arranged in a particular order.
A genome is the complete set of genes of an organism. When proteins are needed, the corresponding genes are transcribed into RNA. RNA is a chain of nucleotides. DNA directs the synthesis of a variety of RNA molecules, each with a unique role in cellular function. The alignment is based on the fact that all living organisms are related by evolution. This implies that the nucleotide (DNA, RNA) and proteins sequences of the species that are closer to each other in evolution should exhibit more similarities. An alignment is the process of lining up sequences to achieve a maximal level of identity, which also expresses the degree of similarity between sequences. Two sequences are homologous if they share a common ancestor. The degree of similarity obtained by sequence alignment can be useful in determining the possibility of homology between two sequences. Such an alignment also helps determine the relative positions of multiple species in an evolution tree, which is called a phylogenetic tree.
