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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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Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
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Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic processes, they can exhibit characteristics of life when infecting a host. Their defining feature is a nucleic acid core, composed of either DNA or RNA, encapsulated within a protein coat called a capsid. This simple structure allows them to invade host cells and use their machinery for replication efficiently.Viral Structure and...
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

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ViMRT: a text-mining tool and search engine for automated virus mutation recognition.

Yuantao Tong1, Fanglin Tan1, Honglian Huang1

  • 1Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

Bioinformatics (Oxford, England)
|November 7, 2022
PubMed
Summary
This summary is machine-generated.

ViMRT accurately extracts virus mutations from scientific literature using NLP. This tool aids vaccine design and drug development by improving mutation recognition.

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Area of Science:

  • Biomedical Informatics
  • Virology
  • Computational Biology

Background:

  • Virus mutations are critical to disease progression, necessitating accurate extraction from scientific literature.
  • Existing mutation extraction methods lack precision and are often based on human gene mutations, limiting their effectiveness for viruses.

Purpose of the Study:

  • To develop an automated text-mining tool for virus mutation recognition.
  • To create a search engine for efficient retrieval of virus mutation information.

Main Methods:

  • Developed ViMRT, a text-mining tool utilizing natural language processing.
  • Implemented 8 optimized rules and 12 regular expressions trained on 830 papers.
  • Validated performance on datasets including influenza and SARS-CoV-2.

Main Results:

  • ViMRT achieved a 99.17% F1-score on a test dataset of 1662 papers.
  • Achieved a 96.99% F1-score when applied to influenza and SARS-CoV-2.
  • Demonstrated superior performance compared to existing tools.

Conclusions:

  • ViMRT is a high-performance method for virus mutation extraction from biomedical literature.
  • The ViMRT search engine facilitates rapid access to virus gene and disease mutation data.
  • ViMRT supports downstream applications like vaccine design and drug development.