Movi:一个快速且缓存效率高的全文pangenome索引
Mohsen Zakeri1, Nathaniel K Brown1, Omar Y Ahmed1
1Department of Computer Science, Johns Hopkins University.
bioRxiv : the preprint server for biology
|November 14, 2023
概括
基因组索引的新工具Movi使用移动结构来快速进行纳米孔测序阅读分类. 它比现有方法提供了显著的加快速度,使实时应用成为可能.
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
- 基因组学就是基因组学.
背景情况:
- 泛基因组索引对于分析大型基因组数据集至关重要,特别是用于快速分类测序读取.
- 现有的压缩索引数据结构,如FM索引和r索引,对复杂的泛基组具有空间和查询时间的限制.
- 移动结构提供了一种新的方法,采用O(r) 空间和O(1) 时间查询,其中r是BWT中运行的次数.
研究的目的:
- 实施和评估Movi,这是一个有效的工具,用于构建和查询移动结构pangenome索引.
- 与现有方法相比,评估Movi在索引大小,查询速度和可扩展性方面的表现.
- 为了证明Movi适合于纳米孔测序中的实时应用.
主要方法:
- 实施的移动结构,用于 pangenome 索引.
- 将Movi与r-index进行比较,以及其他用于索引构建和查询性能的方法.
- 分析索引大小可扩展性随着体大小的增加.
- 对分类任务的查询速度的评估,包括伪匹配长度和向后搜索.
- 缓存性能和内存预检利用率的评估.
主要成果:
- 莫维的索引大小与基BWT中的运行次数 (r) 相对有利,尽管它比较小的引用的r-index大.
- 莫维的查询速度至少比现有的分类任务方法快10倍,在某些情况下比现有的分类任务速度快30倍以上.
- 电影展示了出色的缓存局部性,并从内存预获取中获益,最大限度地减少大 pangenomes 的缓存错误.
- 该工具展示了一个快速的,恒定时间的查询循环,对于实时应用程序至关重要.
结论:
- Movi提供了一个高效的解决方案,用于泛基因组索引和快速阅读分类.
- 在Movi中实现的移动结构为大规模基因组分析提供了显著的性能优势.
- 由于其速度和可预测的查询时间,Movi非常适合实时应用,例如纳米孔测序中的自适应采样.
更多相关视频
10:40Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
10.5K
12:08Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
5.1K
相关概念视频
02:51Multi-species Conserved Sequences
3.9K
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...
3.9K
02:05Gene Evolution - Fast or Slow?
7.1K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.1K
02:54Evolutionary Relationships through Genome Comparisons
5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
02:02Genomics
36.4K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.4K
00:58Genomic DNA in Eukaryotes
47.0K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
47.0K
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
12.5K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.5K