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Updated: Jul 9, 2025

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CodonU:用于Codon使用分析的Python包

Souradipto Choudhuri, Keya Sau

IEEE/ACM transactions on computational biology and bioinformatics

|November 28, 2023

概括

本研究介绍了CodonU,这是一个Python包,用于集成的编码器使用分析 (CUA). 通过提供可重复使用的数据处理和分析工具,与现有格式兼容,CodonU简化了CUA.

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:

目前,Codon使用分析 (CUA) 依赖于多种多样的,分散的工具.
需要一个统一的,可重复使用的软件解决方案,用于CUA数据处理和分析管道.

研究的目的:

开发CodonU,一个全面的Python包,用于整合codon使用分析的各个方面.
为研究人员使用CUA数据提供一个兼容和多功能工具.

主要方法:

开发了CodonU作为一个Python包.
核酸和蛋白质序列的综合统计措施 (例如,编码体适应指数 (CAI),编码体偏差指数 (CBI),tRNA适应指数 (tAI),Gravy分数).
包括对应分析 (COA),图形生成和家族遗传树开发的功能.

主要成果:

CodonU成功地整合了各种CUA工具和统计措施.
该软件包与现有的文件格式兼容,可以独立使用或与其他软件包一起使用.
在Staphylococcus aureus基因组上表现出能力.

结论:

CodonU提供了一个统一而高效的平台,用于编码器使用分析.
该包提高了生物信息学和基因组学研究人员的可用性和可访问性.
CodonU支持多方面的CUA,从基本的统计数据到先进的分析,如家族遗传树的构建.

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From DNA to Protein

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

DNA Base Pairing

DNA Base Pairing

Alternative RNA Splicing

Alternative RNA Splicing

Ribosomal RNA Synthesis

Ribosomal RNA Synthesis

Nucleic Acids

Nucleic Acids

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...