HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.
Bioinformation
; 8(8): 388-90, 2012.
Article
in En
| MEDLINE
| ID: mdl-22570520
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Language:
En
Journal:
Bioinformation
Year:
2012
Document type:
Article
Affiliation country:
Estados Unidos
Publication country:
SG
/
SINGAPORE
/
SINGAPUR
/
SINGAPURA