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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.
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.
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Feb 28, 2012 · Spaced seeds are much more sensitive than the consecutive seed of BLAST and using several seeds represents the current state of the art in approximate search for biological sequences. The most important aspect is computing highly sensitive seeds.
- Silvana Ilie
- silvana@ryerson.ca
- 2012
In particular, PatternHunter demonstrates that an optimized spaced seed improves sensitivity substantially. Accordingly, elucidating the mechanism that confers power to spaced seeds and identifying good spaced seeds are two new issues of homology search. This chapter is divided into six sections.
Oct 24, 2023 · Results. Several algorithms to assist seed generation are presented. The first one finds all permitted spaced seeds iteratively. We observe specific patterns for the seeds of the highest weight. There are often periodic seeds with a simple relation between block size, length of the seed and read.
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.
Sep 16, 2010 · The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome.
