Years and Authors of Summarized Original Work
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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...
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Brejovà B, Brown D, Vinar̆ T (2004) Optimal spaced seeds for homologous coding regions. J Bioinformatics Comput Biol 1:595–610
Buhler J, Keich U, Sun Y (2004) Designing seeds for similarity search in genomic DNA. J Comput Syst Sci 70:342–363
Choi KP, Zhang LX (2004) Sensitivity analysis and efficient method for identifying optimal spaced seeds. J Comput Syst Sci 68:22–40
Choi KP, Zeng F, Zhang LX (2004) Good spaced seeds for homology search. Bioinformatics 20:1053–1059
Intl Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 409:520–562
Keich U, Li M, Ma B, Tromp J (2004) On spaced seeds for similarity search. Discret Appl Math 3:253–263
Li M, Ma B, Kisman D, Tromp J (2004) PatternHunter II: highly sensitive and fast homology search. J Bioinformatics Comput Biol 2:417–440
Ma B, Yao H (2009) Seed optimization for iid similarities is no easier than optimal Golomb ruler design. Inf Process Lett 109(19):1120–1124
Ma B, Tromp J, Li M (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics 18:440–445
Ma B, Li M (2007) On the complexity of the spaced seeds. J Comput Syst Sci 73:1024–1034
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453
Smith TF, Waterman MS (1980) Identification of common molecular subsequences. J Mol Biol 147:195–197
Sun Y, Buhler J (2004) Designing multiple simultaneous seeds for DNA similarity search. In: Proceedings RECOMB’04, 2004, San Diego, pp 76–85
Zhang LX (2007) Superiority of spaced seeds for homology search. IEEE/ACM Trans Comput Biol Bioinformatics (TCBB) 4:496–505
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Zhang, L. (2016). Superiority and Complexity of the Spaced Seeds. In: Kao, MY. (eds) Encyclopedia of Algorithms. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2864-4_803
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