The HIV Database and Analysis Unit provides an integrated repository of HIV sequence and immunological data from publications, by (i) curating and maintaining a relational database with searchable web access for the scientific community, and (ii) developing web-based computational analysis tools for researchers.
The database is located at the Los Alamos National Laboratory, New Mexico and aims to provide to research community a centralized resource of global HIV sequences and information on HIV immune responses.
More information about this resource is available at HIV Databases
Main Areas of Focus
- Data collection providing a comprehensive repository of HIV nucleotide sequences and immunological data.
- Curation, annotation, standardization, validation and quality control of sequences as data is uploaded into the database.
- Access to relational database with searchable web access to extract and analyze data.
- Development of web-based computational analysis tools.
- Listing and providing links to external tools of significance in HIV informatics.
- Making the database information widely available and easily accessible to the research community.
- Publishing annual HIV Sequence and HIV Immunology Compendia, which are available free of charge
Tools
HIV Sequence Database tools are categorized to accomplish:
- Sequence analysis and quality control.
- Sequence alignment and manipulation.
- Phylogenetics.
- Formatting and display of sequences.
HIV Immunology Database tools support to accomplish:
- Analysis of antibody neutralizing activity across viruses.
- Prediction of glycan shielding of HIV Envelope protein.
- Interactive browsing of HIV Envelope immunogen sequences and their mutational consequences
- Evaluation of Human Leukocyte Antigen (HLA)/Major Histocompatibility Complex (MHC) alleles.
- Determination of mosaic HIV immunogen design.
Collaboration Opportunities
- Researchers who have submitted HIV sequences to GenBank can have them added to the HIV Sequence Database. Staff from the HIV Sequence and Immunology Databases encourage collaboration with external groups.
Who Can Use This Resource
- Available for public use
Events
The database training and demonstration workshop is held annually at HIV Keystone symposium and Immune Epitope Database (IEDB) User Workshop to:
- Train researchers in the use of HIV sequence and immunology databases functionality.
- Publicize the availability of services offered.
- Solicit suggestions for improvement/expansion of the resource.
Featured Research
- Guiding scientific community to retrieve, align and analyze lentiviral sequences and immunological data from the relational database resource, to aid in the development of vaccines and therapies, and in understanding of pathology, genetics, and evolution of HIV.
- Currently, HIV Sequence Database includes 1,240,044 sequences, while HIV Immunology Database includes 12,670 CTL/CD8+ epitope records, 1,695 T-helper/CD4+ epitope records, and 4,579 antibodies.
- Expanded scope of HIV Database and Analysis Unit includes (i) addition of sequences and immunological information for HIV Envelope immunogens in an interactive browser, (ii) display of immunological determinants, including T cell epitopes and antibody binding sites, in interactive HIV Genome Browser, and (iii) inclusion of a database of sequences from clonal lineages of HIV broadly neutralizing antibodies.
- Updated summary of data contained in the database is published yearly in HIV Sequence and Immunology Compendia.
- Organizing the database training and demonstration workshop yearly at scientific symposia to present HIV Database and Analysis Unit functionality.