TY - GEN
T1 - HPVdb
T2 - 2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
AU - Zhang, Guang Lan
AU - Riemer, Angelika
AU - Keskin, Derin B.
AU - Chitkushev, Lou
AU - Reinherz, Ellis L.
AU - Brusic, Vladimir
N1 - Copyright:
Copyright 2013 Elsevier B.V., All rights reserved.
PY - 2013
Y1 - 2013
N2 - High-risk human papilloma viruses (HPV) are the causes of many cancers, including cervical, anal, vulvar, vaginal, penile and oropharyngeal. To facilitate diagnosis, prognosis, and characterization of these cancers, we constructed the Human Papillomavirus T cell Antigen Database (HPVdb). It contains 2865 curated antigen entries of antigenic proteins derived from 18 genotypes of high-risk HPV and 18 genotypes of low-risk HPV. HPVdb also catalogs 96 verified T cell epitopes and 45 verified HLA ligands. Primary amino acid sequences of HPV antigens were collected and annotated from UniProtKB. T cell epitopes and HLA ligands were collected from data mining of scientific literature. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). A set of computational tools for in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, classification of HPV types based on cancer risk, and T cell epitope/HLA ligand visualization, have been integrated in HPVdb. Predicted Class I and Class II HLA binding peptides for 15 common HLA alleles are included in this database as putative targets. HPVdb is a specialized database that integrates curated data and information with tailored analysis tools to facilitate data mining to aid rational vaccine design by discovery of vaccine targets. To our best knowledge, HPVdb is a unique data source providing a comprehensive list of antigen peptides in HPV.
AB - High-risk human papilloma viruses (HPV) are the causes of many cancers, including cervical, anal, vulvar, vaginal, penile and oropharyngeal. To facilitate diagnosis, prognosis, and characterization of these cancers, we constructed the Human Papillomavirus T cell Antigen Database (HPVdb). It contains 2865 curated antigen entries of antigenic proteins derived from 18 genotypes of high-risk HPV and 18 genotypes of low-risk HPV. HPVdb also catalogs 96 verified T cell epitopes and 45 verified HLA ligands. Primary amino acid sequences of HPV antigens were collected and annotated from UniProtKB. T cell epitopes and HLA ligands were collected from data mining of scientific literature. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). A set of computational tools for in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, classification of HPV types based on cancer risk, and T cell epitope/HLA ligand visualization, have been integrated in HPVdb. Predicted Class I and Class II HLA binding peptides for 15 common HLA alleles are included in this database as putative targets. HPVdb is a specialized database that integrates curated data and information with tailored analysis tools to facilitate data mining to aid rational vaccine design by discovery of vaccine targets. To our best knowledge, HPVdb is a unique data source providing a comprehensive list of antigen peptides in HPV.
KW - Human papilloma viruses
KW - Immunological databases
KW - T cell epitopes
KW - Vaccine target discovery
KW - Viral antigens
UR - http://www.scopus.com/inward/record.url?scp=84888175517&partnerID=8YFLogxK
U2 - 10.1145/2506583.2512360
DO - 10.1145/2506583.2512360
M3 - Conference contribution
AN - SCOPUS:84888175517
SN - 9781450324342
T3 - 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
SP - 843
EP - 848
BT - 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Y2 - 22 September 2013 through 25 September 2013
ER -
