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相关概念视频

Evolutionary Relationships through Genome Comparisons02:54

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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...
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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...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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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...
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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使用nf-core/pangenome进行集群效率的万科组图形构造.

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nf-core/pangenome 是一个用于构建 pangenome 图的新管道. 它提供了一种可扩展和高效的参考无偏见的方法,与现有方法相比,实现了显著的加快速度.

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科学领域:

  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 泛基因组图可以捕捉基因组的变异性,但目前的方法有偏差和可扩展性问题.
  • 像PanGenome Graph Builder (PGGB) 这样的现有工具可以排除复杂的序列或依赖引用.
  • 需要一个最先进的管道,以方便部署,高效的资源使用和可扩展性.

研究的目的:

  • 介绍一下nf-core/pangenome,这是一个用于构建pangenome图的新型管道.
  • 为 pangenome 图形构建提供了一个参考无偏,可扩展和高效的解决方案.
  • 为了解决现有的万科组图构建方法的局限性.

主要方法:

  • 按照 nf-core 的最佳实践在 Nextflow 中实施.
  • 使用生物容器在高性能计算 (HPC) 环境中实现便携性和部署.
  • 在集群节点之间分配对齐,以提高可扩展性.

主要成果:

  • 成功构建了1000个人类染色体的泛基因组图,19个单元型和2146个大肠杆菌序列.
  • 与PGGB相比,实现了两到三倍的速度.
  • 证明有效利用资源而不会增加温室气体排放.

结论:

  • nf-core/pangenome在pangenome图形构建方面提供了显著的进步.
  • 管道提供了一个可扩展,高效和参考无偏的方法.
  • 它很容易部署,可以在各种计算环境中使用.