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Oct 24, 2023 · In ZOOM software , spaced seeds are generated to perform alignment with at most two mismatches. In PerM software , the authors used so-called periodic spaced seeds to improve mapping efficiency. Fast alignment-free string comparison based on spaced seeds (spaced-words) is discussed in .
Sep 1, 2008 · We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able...
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We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able to map the Illumina/Solexa reads of 15X coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.
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.
Aug 6, 2008 · ZOOM starts by hashing the reads set using the spaced seeds set, one hash table for a seed. Each read is indexed and stored according to the hash keys generated by these seeds. A hash key is translated from the nucleotide letters picked at positions that correspond to 1-positions in a spaced seed.
- Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li
- 2008
A spaced seed is a given pattern such as 11*1**11**1*1*1111. The number of 1-positions is called the weight of the seed. Different spaced seeds have different hit probabilities in a randomly sampled similarity. In PatternHunter (see G6G Abstract Number 20379 ), one or several optimized spaced seeds are determined.
To circumvent this problem, it is possible to use spaced seeds (as it is implemented in ZOOM [Lin et al., 2008], BFAST, GASSST, SHRiMP2, or PerM, for instance), i.e., seeds with so-called “don't care” positions. A “don't care” position, “x”, is a position in the read where the algorithm does not check the type of nucleotide present.
