细菌基因组学的一个生物信息生态系统:PhaMMSeqs,Phamerator,pdm_utils,PhagesDB,DEPhT和PhamClust
Christian H Gauthier1, Graham F Hatfull1
1Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Viruses
|August 29, 2024
概括
计算工具已经在分析菌体 (菌体) 基因组方面取得了重大进展,帮助研究和教育社区了解菌体进化和马赛克主义. 这些生物信息学资源免费提供给更广泛的科学界.
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.
- 微生物学 微生物学
- 进化生物学 进化生物学
背景情况:
- 在过去的三十年中,细菌菌体基因组的测序数量大幅增加.
- 基因组测序的技术进步和成本降低加速了菌体基因组学研究.
- 像SEA-PHAGES和PHIRE这样的综合研究教育计划对菌体基因组数据库做出了重大贡献.
研究的目的:
- 描述用于分析菌体基因组数据的计算和生物信息工具.
- 突出这些工具在研究和教育社区中的应用.
- 为更广泛的科学界强调这些工具的可用性.
主要方法:
- 利用一套计算和生物信息工具进行菌体基因组分析.
- 用于整合和分析来自不同来源的菌体基因组数据的应用工具.
- 采用了从细菌基因组中识别和提取prophages的方法.
- 用于计算基因家族 ("家族") 和分析基因组马赛克的工具.
主要成果:
- 在RefSeq数据库中,SEA-PHAGES和PHIRE对25%的完整菌体基因组负责.
- 描述的工具有助于分析复杂的核酸和氨基酸马赛克在菌体基因组.
- 超过5万名学生已经从这些研究和教育工具中受益.
结论:
- 复杂的计算和生物信息工具对于推动菌体基因组学的发展至关重要.
- 这些工具可以提供详细的进化见解和对菌体基因组结构的理解.
- 这些工具是免费访问的,促进了菌体研究社区的更广泛采用和贡献.
相关概念视频
01:30Lytic Cycle of Bacteriophages
70.5K
Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
70.5K
00:43Lysogenic Cycle of Bacteriophages
62.0K
In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
62.0K
02:54Evolutionary Relationships through Genome Comparisons
5.7K
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...
5.7K
02:53CRISPR and crRNAs
16.9K
Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
16.9K