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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.
Feb 28, 2012 · A spaced seed is any string containing 1's and *'s. Since having a * at one end of a seed is not useful, we assume that all seed start and end with a 1. For a seed s, the weight w of s is the number of 1's and the length ℓ is the number of all letters. The i th letter of s is denoted s [ i ].
- Silvana Ilie
- silvana@ryerson.ca
- 2012
Jun 4, 2013 · One consequence of this is that spaced seeds tell you more about reads than non-spaced ones (the way that a fingerprint tells you more about the body it comes from than a fingerprint-sized patch of elbow skin would). An example: spaced vs. non-spaced seeds.
Nov 30, 2018 · Fundamental concepts on spaced seeds Definition 1 (Spaced seed.) A spaced-seed S (or just a seed) is a binary string of length k, where the symbol ‘1’ requires a match in that position, while a symbol ‘0’ allows for “don’t care”. A spaced seed is characterized by its length k and by its weight W<k, which is the number of 1s in the ...
- Samuele Girotto, Matteo Comin, Cinzia Pizzi
- 2018
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Figure 14.2: Spaced k-mer method of mapping reads to reference genome of the algorithm. Using smaller k-mer seeds allows for less precise base pair matching (greater sensitivity), but requires more matches to be attempted. Smaller seeds take up less memory, while larger seeds run faster.
Jan 1, 2016 · A spaced seed is optimal for aligning sequences with identity p of length n if it has the largest hit probability over a uniform region of length n in which 1 appears with probability p at a position.
Oct 24, 2023 · Spaced seeds (masks ignoring symbols at specific locations) are a way to approach the task. An ideal (full sensitivity) spaced seed should enable us to find all such positions subject to a given maximum number of mismatches permitted. Results. Several algorithms to assist seed generation are presented.
