title: HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.
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.
authors.affiliation: Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA. yin@pathology.ufl.edu
authors.forename: Li
authors.initials: L
authors.lastname: Yin
authors.forename: Jiqiang
authors.initials: J
authors.lastname: Yao
authors.forename: Brent P
authors.initials: BP
authors.lastname: Gardner
authors.forename: Kaifen
authors.initials: K
authors.lastname: Chang
authors.forename: Fahong
authors.initials: F
authors.lastname: Yu
authors.forename: Maureen M
authors.initials: MM
authors.lastname: Goodenow