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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Published on: May 26, 2013

Viral genome analysis and knowledge management.

Carla Kuiken1, Hyejin Yoon, Werner Abfalterer

  • 1Los Alamos National Laboratory, Theoretical Biology and Biophysics (MS K710), Los Alamos, NM, USA. kuiken@lanl.gov

Methods in Molecular Biology (Clifton, N.J.)
|November 30, 2012
PubMed
Summary
This summary is machine-generated.

This study details the infrastructure supporting the HIV, HCV, and HFV databases, crucial for global genetic data analysis and sequence annotation. These platforms ensure data accessibility and quality for researchers worldwide.

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Area of Science:

  • Bioinformatics
  • Genomic Data Management
  • Virology

Background:

  • Global genetic data analysis faces challenges in integrating information from diverse sources and interfaces.
  • The HIV, Hepatitis C Virus (HCV), and Hemorrhagic Fever Virus (HFV) databases aim to provide accessible, high-quality viral sequence and annotation data.

Purpose of the Study:

  • To describe the infrastructure sustaining long-term operation of the HIV, HCV, and HFV analysis platforms.
  • To highlight the processes ensuring data quality, accessibility, and usability for researchers.

Main Methods:

  • Distilling gene and protein sequences from GenBank using submitter and script-generated annotations.
  • Generating, manually curating, and iteratively refining nucleotide and amino acid sequence alignments.
  • Parsing and validating epidemiological and clinical information for database integration.

Main Results:

  • Development and maintenance of robust data processing pipelines for sequence quality control and annotation.
  • Iterative refinement of sequence alignments leading to improved accuracy.
  • Continuous updates to user interfaces based on user feedback and requests.

Conclusions:

  • The described infrastructure has ensured the vitality and utility of these critical viral databases for nearly 25 years.
  • Active use by database staff is key to identifying and resolving issues, driving platform improvements.
  • These platforms provide essential resources for global viral genetic data analysis.