Related Experiment Video
Updated: Nov 17, 2025
14:06
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
15.5K
Syncmers are more sensitive than minimizers for selecting conserved k‑mers in biological sequences
1None, Corte Madera, CA, USA.
Peerj
|February 19, 2021
Summary
Syncmers offer a novel k-mer selection method for biological sequences, outperforming traditional minimizers in density and conservation. This advancement impacts read mapping and taxonomy prediction.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Minimizers are standard for selecting fixed-length substrings (k-mers) in biological sequence analysis.
- Existing methods like minimizers are susceptible to mutations, potentially affecting downstream applications.
- Applications include read mapping, taxonomy prediction, and large dataset indexing.
Purpose of the Study:
- Introduce syncmers as an alternative k-mer selection strategy.
- Compare syncmer performance against minimizers in terms of density and conservation.
- Evaluate syncmers for their robustness against sequence mutations.
Main Methods:
- Defined syncmers based on the position of the smallest substring (s-mer) within a k-mer.
- Introduced 'closed syncmers' requiring the smallest s-mer at the k-mer's boundaries.
- Tested syncmers using parameters from minimap2 and Kraken, comparing with minimizers.
Main Results:
- Syncmers achieve lower k-mer density compared to minimizers.
- Syncmers demonstrate higher sequence conservation than minimizers.
- Syncmers are robust against mutations, unlike minimizers.
Conclusions:
- Syncmers provide a synchronized and mutation-resistant k-mer selection method.
- Syncmers offer simultaneous improvements in density and conservation over minimizers.
- This method enhances reliability in biological sequence analysis tools.
Related Concept Videos
02:51Multi-species Conserved Sequences
4.4K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.4K
02:26Conservation of Protein Domains Over Different Proteins
13.6K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.6K
01:05Maxam-Gilbert Sequencing
11.9K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
11.9K
01:49Conserved Binding Sites
1.8K
1.8K
01:49Conserved Binding Sites
4.8K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.8K
01:02¹H NMR: Interpreting Distorted and Overlapping Signals
1.2K
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
1.2K