プログレッシブ・カクタスは,千のゲノム時代のための多重ゲノムアライナーです
Joel Armstrong1, Glenn Hickey1, Mark Diekhans1
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA.
Nature
|November 12, 2020
まとめ
ゲノム解析の新しい方法は,シーケンシングデータの急速な増加のために必要である. プログレッシブ・カクタスは,何千もの脊椎動物のゲノムを 高い精度で 参照フリーで並べることができます
科学分野:
- ゲノミクス
- バイオ情報学
- コンピュータ生物学
背景:
- 配列のコストは減り,第3世代の技術は改善され,新しいゲノムアセンブリが急速に増加しました.
- NCBIのデータベースでは,2018年7月から2019年7月までの間,脊椎動物のゲノムアセンブリが50%以上増加しました.
- 新しい人間の de novo アセンブリは,小さなポリモルフィズムと大きな構造的差異の分析を可能にします.
研究 の 目的:
- 進化の洞察のためのゲノムデータの前例のないスケールによって引き起こされる課題に取り組むこと
- 既存のゲノム分析方法をデータスケールの拡大に適応させる.
- 拡張可能な複数のゲノムアラインメントプログラムを開発する
主な方法:
- カクタスのプログラムに 漸進的な拡張が施され 参照のない多重ゲノムアラインメントツールです
- 改良されたプログラム"プログレッシブ・カクタス"は 数万から数千の大きな脊椎動物のゲノムを 処理するように設計されました
- この方法は600以上の胎児のゲノム配列でテストされました
主要な成果:
- プログレッシブ・カクタスは 数十から数千の大きな脊椎動物のゲノムを 参照なしで並べることができます
- プログラムでは大量のゲノムでも 高いアライメント品質を維持しています
- この研究は,これまでに最大規模で 多数の脊椎動物のゲノム配列を 600以上の胎児ゲノムで達成した.
結論:
- プログレッシブ・カクタスは,複数のゲノムアラインメントのための以前の方法のスケーラビリティの制限を克服します.
- 開発された方法は,大規模なゲノムデータの分析を容易にし,ゲノム進化に関する新しい洞察を可能にします.
- 比較ゲノミクスの限界を押し広げました 比較ゲノミクスの限界を押し上げました
さらに関連する動画
08:03Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
2.6K
09:06High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
Published on: October 5, 2018
10.6K
関連する概念動画
Evolutionary Relationships through Genome Comparisons
6.7K
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...
6.7K
Multi-species Conserved Sequences
4.5K
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...
4.5K
Gene Duplication and Divergence
7.5K
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.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
7.5K
Genome Annotation and Assembly
20.0K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.0K
Genomics
39.0K
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...
39.0K
Next-generation Sequencing
96.3K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
96.3K
