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Title

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set

 

Authors

Li Yin1*, Jiqiang Yao2, Brent P Gardner1, Kaifen Chang1, Fahong Yu2 & Maureen M Goodenow1

 

Affiliation

1Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL; 2Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL

 

Email

yin@pathology.ufl.edu; *Corresponding author

 

Article Type

Database

 

Date

Received Apr 18, 2012; Accepted April 19, 2012; Published April 30, 2012

Abstract

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

 

Availability

http://www.ijbcb.org/HPV/

 

Keywords

Human papilloma virus, Genotyping; web-based, Blast search, Next Generation sequencing

 

Citation

Yin et al. Bioinformation 8(8): 388-390 (2012)

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.