(m,n) -mer-一个用于序列分类的简单统计特征
Amanda Araújo Serrão de Andrade1, Marco Grivet2, Otávio Brustolini1
1Bioinformatics Laboratory (LABINFO), National Laboratory for Scientific Computing, Av. Getulio Vargas, 333-Quitandinha, 25651-076, Rio de Janeiro, Brazil.
Bioinformatics advances
|July 14, 2023
概括
该研究引入了 (m,n) -mer频率作为k-mers的高级分类特征. 这种新方法提高了序列分类任务的性能,特别是对于较短的序列和较小的k值.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 机器学习 机器学习
背景情况:
- 传统的k-mer频率特征被广泛用于序列分类.
- 在k-mer性能上存在局限性,特别是在复杂的数据集和更短的序列方面.
研究的目的:
- 为了比较 (m,n) -mer频率特征与传统的k-mer特征的性能.
- 评估 (m,n) -mers在各种分类任务中的有效性,包括二进制,多类和聚类.
- 引入 (m,n) -mer频率作为一个潜在的更强大的特征,用于序列分析.
主要方法:
- 用11个不同的生物数据集进行比较分析.
- 实施并比较k-mer和 (m,n) -mer频率特征提取方法.
- 在二进制,多类和集群分类场景中评估性能指标.
主要成果:
- (m,n) -mer频率特征在多个数据集和分类类型中表现出卓越的性能.
- 与k-mers相比,使用 (m,n) -mers时观察到具有统计学意义的改善.
- (m,n) -mers在分类较短的序列 (低至300bp) 和较小的k值 (2-4) 中特别出色.
结论:
- (m,n) -mer频率是识别生物序列中复杂的歧视性模式的有效特征.
- 这种方法提供了更高的分类准确性,特别是对于具有挑战性的数据集和序列长度.
- 该 (m,n) -mer算法作为R包和GitHub上可供社区使用.
更多相关视频
相关概念视频
Modern Molecular Taxonomy
53
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
53
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule
1.4K
In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1 triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the...
1.4K
Multiple Comparison Tests
3.9K
Multiple comparison test, abbreviated as MCT, is a post hoc analysis generally performed after comparing multiple samples with one or more tests. An MCT will help identify a significantly different sample among multiple samples or a factor among multiple factors.
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...
3.9K
Multi-species Conserved Sequences
4.0K
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...
4.0K
Sanger Sequencing
754.9K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
754.9K
Per-Unit Sequence Models
98
An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...
98


