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- Efficient seed spacing offers a range of benefits that contribute to the well-being and productivity of your garden. By providing adequate space, you enable each plant to access the necessary sunlight, nutrients, water, and air circulation, thus reducing competition and promoting healthy growth.
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Why are spaced seeds important in bioinformatics?
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Spaced seeds allow for even more permissive local matching by allowing certain base pairs (defined by the pattern of the specific spaced seed) to mismatch without penalty, thus allowing algorithms that use the general "hit-extend" strategy of alignment to explore additional potential matches that would be otherwise ignored.
Nov 30, 2018 · Spaced-seeds, i.e. patterns in which some fixed positions are allowed to be wild-cards, play a crucial role in several bioinformatics applications involving substrings counting and indexing, by often providing better sensitivity with respect to k -mers based approaches.
- Samuele Girotto, Matteo Comin, Cinzia Pizzi
- 2018
Sep 16, 2010 · SHRiMP [ 9] uses spaced seeds that can hit at any position of the read and introduces a lower bound on the number of hits within one read. MAQ [ 3] uses six light-weight seeds allowed to hit in the initial part of the read.
- Laurent Noé, Marta Gîrdea, Gregory Kucherov
- 10.1155/2010/708501
- 2010
- Adv Bioinformatics. 2010; 2010: 708501.
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
- 10.1186/1756-0500-5-123
- 2012
- BMC Res Notes. 2012; 5: 123.
Dec 1, 2014 · Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances, and to provide a lower misclassification rate when used with Support Vector Machines (SVMs).
- Laurent Noé, Donald E. K. Martin
- 10.1089/cmb.2014.0173
- 2014
- J Comput Biol. 2014 Dec 1; 21(12): 947-963.
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. Several algorithms to assist seed generation are presented.
Results: Within this general framework, we show that spaced seeds provide a significant improve- ment of classification accuracy, as opposed to traditional contiguous k-mers. We support this the- sis through a series of different computational experiments, including simulations of large-scale metagenomic projects.
