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Ribosome Profiling02:24

Ribosome Profiling

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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...
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary 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...
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相关实验视频

Updated: Jun 3, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K

SProtFP:一种基于机器学习的方法,用于对 prokaryotes 中的小 ORF 的功能分类.

Akshay Khanduja1, Debasisa Mohanty1

  • 1National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.

NAR genomics and bioinformatics
|January 9, 2025
PubMed
概括

我们开发了SProtFP,这是一种用于注释小细菌蛋白和识别抗菌的机器学习工具. 这种方法有助于了解微生物群落中未表征的蛋白质的功能.

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.
  • 计算生物学 计算生物学

背景情况:

  • 小蛋白质 (≤100氨基酸) 在所有生命形式中都至关重要.
  • 这些小蛋白质的功能性注释,特别是在 prokaryotes 中,仍然具有挑战性.
  • 识别新的小蛋白及其功能对于理解微生物生物学至关重要.

研究的目的:

  • 开发一种基于机器学习的方法,SProtFP,用于 prokaryotic 小蛋白的功能注释.
  • 为了能够识别小型开放式读取框架 (smORF) 编码的抗微生物 (AMP).
  • 为了促进微生物组数据集的大规模功能注释,特别是那些具有低序列同质性的数据集.

主要方法:

  • SProtFP使用在物理化学描述器上训练的独立人工神经网络 (ANN).
  • 分类类别包括抗毒素2型,细菌素,DNA结合,金属结合,核糖体蛋白,RNA结合,1型毒素和2型毒素蛋白.
  • 一个单独的模型被训练用于识别smORF编码的抗微生物 (AMP).

主要成果:

  • 在试验组中,SProtFP实现了高性能,平均ROC-AUC为0.92 (10倍交叉验证) 和0.94/0.93.
  • 该方法成功识别了成千上万的远程同类物质,并在人类肠道微生物组数据中为未表征的蛋白质分配了功能.

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相关实验视频

Last Updated: Jun 3, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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

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  • 对于微生物组数据集的大规模注释的实用性已被证明,即使具有低序列同质性.

    • 结论:

    • SProtFP 是一种有效的工具,用于对 prokaryotic 小蛋白和 smORF 编码的 AMP 的功能注释.
    • 该方法显著提高了新型小蛋白及其在微生物群落中的功能的发现.
    • SProtFP 在线可用,可与其他基因组注释工具集成,用于全面分析.