相关实验视频

Updated: Jul 11, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

在元基因组时代的RefSeq和 prokaryotic基因组注释管道

Daniel H Haft¹, Azat Badretdin¹, George Coulouris¹

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Nucleic acids research

|November 14, 2023

概括

国家生物技术信息中心 (NCBI) RefSeq数据库现在包括超过17000个高质量的元基因组组装基因组 (MAGs),增强了细菌和考古基因组的多样性. 通过更好的基因检测和扩展功能信息,注释质量得到了改善.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

国家生物技术信息中心 (NCBI) 参考序列 (RefSeq) 数据库是细菌和古生物基因组和蛋白质的全面资源.
保持高质量,最新的注释对于基因组研究至关重要.

研究的目的:

增强RefSeq数据库的多样性和质量.
为了改善 prokaryotic 基因组的注释.

主要方法:

从INSDC提交的高质量的元基因组组装基因组 (MAG) 的包含.
对组装质量,污染和注释完整性进行严格的验证检查.
为改善基因检测和功能性注释,更新了原生物基因组注释管道 (PGAP).

主要成果:

现在RefSeq包括超过17000个MAG,代表着各种各样的 prokaryotic 序列和家族.
注释准确性有所提高,83%的蛋白质是由精选的蛋白质家族模型命名的.
基因本体学 (GO) 术语现在被分配给48%的RefSeq蛋白质,促进了比较基因组学.

结论:

该RefSeq数据库已经显著扩大了其 Prokaryotic 基因组的集合,特别是通过 MAGs 的整合.
增强的注释管道和质量控制措施确保为科学界提供高质量的信息资源.

更多相关视频

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

相关概念视频

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...