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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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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...
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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Hybridoma technology is used for the large-scale production of monoclonal antibodies. Monoclonal antibodies bind to only a single antigenic determinant or epitope. Such antibodies are used in research, diagnostics, and disease therapy. The hybridoma technology established in 1975 by Georges Köhler and Cesar Milstein was awarded the Nobel Prize in Medicine in 1984 for revolutionizing research and therapy.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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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.
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病毒预测器:基于XGBoost的软件,用于预测人类数据中的病毒相关序列.

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我们开发了VirusPredictor,这是一款机器学习工具,用于识别患者数据中的未知病毒序列. 该软件准确地分类序列,有助于发现新型传染性病毒和内源逆转录病毒.

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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.
  • 机器学习 机器学习

背景情况:

  • 鉴定没有参考基因组的新型病毒是具有挑战性的,因为高通量数据中的不可映射的序列.
  • 现有的软件缺乏专门的能力来准确预测人类样本中的病毒序列.

研究的目的:

  • 从人类数据开发和验证一种机器学习方法,用于从人类数据中预测病毒序列,包括未表征的病毒和内源逆转录病毒 (ERV).
  • 创建一个用户友好的软件工具,VirusPredictor,用于准确分类无法映射的序列.

主要方法:

  • 开发了一个两步的XGBoost分类模型,利用内部病毒基因组数据库.
  • 第一步将序列分为传染性病毒,ERV或非ERV人类类别.
  • 第二步进一步将传染性病毒序列分为六个分类学子组.

主要成果:

  • 预测准确度随着序列长度的增加而增加,在序列>2000bp时达到0.98.
  • 根据序列长度,传染性病毒的分类精度从0.92到>0.98不等.
  • 病毒预测器在应用于真实基因组和元基因组数据集时表现出高准确性.
  • 这项研究是第一个将ERV分类到传染性病毒序列预测中,并将病毒子组预测结合起来.

结论:

  • 病毒预测器准确地预测了人类数据中无法映射的序列的起源,包括新型病毒和ERV.
  • 较长的序列 (理想情况下>850 bp) 提高了预测准确性;建议对短读数进行 de novo 组装.
  • 病毒预测器是一个有价值的开源工具,用于推进病毒发现和诊断.