Superiority and Complexity of the Spaced Seeds

Years and Authors of Summarized Original Work

• 2006; Ma, Li, Zhang

Problem Definition

In the 1970s, sequence alignment was introduced to demonstrate the similarity of the sequences of genes and proteins [12]. A DNA sequence is a finite sequence over four nucleotides – adenine, guanine, cytosine, and thymine, whereas a protein sequence is over 20 amino acids. Homologous proteins have similar biological functions. Since they evolve from a common ancestral sequence, the sequences of homologous proteins and their encoding genes are often highly similar. Therefore, the DNA or amino acid sequence of a protein is often aligned with the sequences of well-studied proteins to infer the biological functions of the protein.

Formally, an alignment of two sequences, S and T, on an alphabet $\mathcal{B}$ is a two-row matrix with the following properties:

• 1. The letters in Sare listed in order, interspersed with space symbols “–,” in a row, where “–” represents the fact that a letter is missing at...