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An animated example to show the utility of a spaced seed. First, an attempt to identify a local candidate match without a space seed is made (unsuccessfully), before attempting the same task with a simple spaced seed, where a hit is found successfully. Green indicates a matching base position. See here for more details.
In bioinformatics, a spaced seed is a pattern of relevant and irrelevant positions in a biosequence and a method of approximate string matching that allows for substitutions. They are a straightforward modification to the earliest heuristic-based alignment efforts that allow for minor differences between the sequences of interest. Spaced seeds have been used in homology search.,[1] alignment,[2] assembly,[3] and metagenomics.[4] They are usually represented as a sequence of zeroes and ones, where a one indicates relevance and a zero indicates irrelevance at the given position. Some visual representations use pound signs for relevant and dashes or asterisks for irrelevant positions.
^Ma, Bin; Tromp, John; Li, Ming (March 2002). "PatternHunter: faster and more sensitive homology search". Bioinformatics. 18 (3): 440–445. doi:10.1093/bioinformatics/18.3.440. PMID 11934743.
^Birol, I; Chu, J; Mohamadi, H; Jackman, S. D.; Raghavan, K; Vandervalk, B. P.; Raymond, A; Warren, René L. (2015). "Spaced Seed Data Structures for De Novo Assembly". International Journal of Genomics. 2015: 196591. doi:10.1155/2015/196591. PMC 4619942. PMID 26539459.
"SpaceSeed" is the 22nd episode of the first season of the American science fiction television series Star Trek. It was first broadcast by NBC on February...
In bioinformatics, a spacedseed is a pattern of relevant and irrelevant positions in a biosequence and a method of approximate string matching that allows...
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