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HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation
Li Yin1, Jiqiang Yao, Brent P Gardner
1Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA. yin@pathology.ufl.edu
Bioinformation
|May 10, 2012
Summary
Next Generation Sequencing (NGS) for human papillomavirus (HPV) detection is advanced by HPV-QUEST, a rapid genotyping system. This tool aids molecular epidemiology studies of multiple HPV infections with an updated sequence database.
Area of Science:
- Virology
- Molecular Epidemiology
- Bioinformatics
Background:
- Next Generation Sequencing (NGS) offers sensitive detection of multiple human papillomavirus (HPV) infections.
- Existing genotyping systems lack comprehensive updated HPV reference sequences and capacity for NGS data.
Purpose of the Study:
- To develop an automated and rapid HPV genotyping system to address the limitations of current methods.
- To create a web-based tool for efficient analysis of HPV molecular epidemiology.
Main Methods:
- Developed HPV-QUEST, a web-based automated genotyping system using HTML, PHP, Perl, and MySQL.
- Integrated a comprehensive database of annotated HPV reference sequences (150+ types across 5 genera, 14 species).
- Algorithm designed to genotype query sequences by blasting against the reference database.
Main Results:
- HPV-QUEST processes up to 10 megabases of sequence data within 1-2 minutes.
- Provides detailed genotyping results including genus, species, type, infection site, and risk.
- Outputs results in HTML, text, and Excel formats, including e-value, blast score, and identity metrics.
Conclusions:
- HPV-QUEST is an efficient and rapid automated system for HPV genotyping from NGS data.
- The system enhances the investigation of HPV molecular epidemiology, particularly for multiple infections.
- Provides comprehensive and analysis-ready data for further research.
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