Analytical and Computational Tools
- HIV Databases
- ELF/Epitope Location Finder
Search a submitted protein sequence for known epitopes from our immunology databases; epitopes predicted by consensus binding motifs; and epitopes predicted by the IEDB binding algorithm. - Hepitope/HLA-Enriched Possible Epitope
The Hepitope tool searches for hopeful-epitopes or "Hepitopes." - HLA Analysis Tools
These tools calculate and graph HLA frequencies in a population; search for HLA linkage disequilibrium in a population; and compare the HLA frequencies in two populations. - Human Immunology Project Consortium
The HIPC capitalizes on recent advances in immune profiling methods to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s). - Mosaic Vaccine Tool Suite
The three tools that make up this suite allow users to design and assess vaccine candidate protein sequences. - Motif Scan/HIV HLA Anchor Residue Motifs
This page serves three functions: 1) find HLA anchor residue motifs within protein sequences for specified HLA genotypes, serotypes, or supertypes; 2) search any single protein for all known HLA anchor residue motifs; and 3) view motif libraries. - PepMap
The PepMap tool maps an input set of peptides on the HIV reference sequence HXB2.
- ELF/Epitope Location Finder
- Immune Epitope Database and Analysis Resource (IEDB)
- B Cell Epitope Prediction Tools
These tools predict IC50 values for peptides binding to specific MHC molecules. - T Cell Epitope Prediction Tools
These tools predict IC50 values for peptides binding to specific MHC molecules. - Epitope Cluster Analysis
This tool groups epitopes into clusters based on sequence identity. - Epitope Conversancy Analysis
This tool computes the degree of conservancy of an epitope within a given protein sequence set at a given identity level. - Epitope Sequence and 3D Structural Homology Mapping
A tool for immunologists to study the three dimensional structural features of an epitope sequence and its source sequence. - Population Coverage Calculation
The tools are intended for the detailed analysis of a known epitope sequence or group of sequences.
- B Cell Epitope Prediction Tools
- MHC Sequence Feature Variant Type (SFVT) Analysis
This analysis enables genetic association analysis of classical HLA protein sub-regions defined with structural (e.g., helix) and functional (e.g., binding site) information.
Databases and Data Sets
- HIV Database
- Antibody Database
HIV molecular immunology database - CTL/CD8+ T-Cell Epitope Database
HIV molecular immunology database - Epitope Alignments
The alignments are FASTA files of the unique epitope sequences aligned to the LANL HIV subtype reference alignments. - Epitope Tables
These tables summarize the epitopes from the database. - HLA Analysis Tools
These tool calculate and graph HLA frequencies in a population; search for HLA linkage disequilibrium in a population; and compare the HLA frequencies in two populations - HLA Typing and Epitope Mapping
These data tables describe: peptides; subjects (e.g., each person's HLA and reactive peptides); and maps of overlapping peptides and HLA types of responding individuals. - Motif Scan/HIV HLA Anchor Residue Motifs
This page serves three functions: 1) find HLA anchor residue motifs within protein sequences for specified HLA genotypes, serotypes, or supertypes; 2) search any single protein for all known HLA anchor residue motifs, and 3) view motif libraries. - SVG Epitope Maps
These maps are implemented with SVG (scalable vector graphics), which is supported by most, but not all, major web browsers. - T Helper/CD4+ T-Cell Epitope Database
The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials.
- Antibody Database
- Immune Epitope Database and Analysis Resource (IEDB)
The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. - MHC Allele Search
Complete DNA and protein sequences, sequence features, and population frequencies of MHC alleles. - Immune Epitope Search
Search for experimentally determined and predicted epitopes. - ViPR Search
The Virus Pathogen Resource is a useful resource for the virology research community designed to assist users with various projects involving sequence and structure analysis, comparative genomics, and virus phenotype studies among others.
Visualization and Modeling Tools
- HLA Analysis Tools
These tools calculate and graph HLA frequencies in a population; search for HLA linkage disequilibrium in a population; and compare the HLA frequencies in two populations - Immunology Database and Analysis Portal (ImmPORT)
- Protein Feature Accent
View 3D structures of HIV proteins and map a desired sequence (e.g., short functional domain or epitope) directly onto the interactive graphic.
Contact Information
For more information on Bioinformatics-Epitopes and MHC/HLA Resources, email:
Bioinformatics and Computational Sciences Branch
Content last reviewed on April 20, 2012