HIV Molecular Immunology Database: Tools & Links

Tools produced by the Los Alamos HIV Database

• Epilign Align amino acid epitopes against our alignments
• PeptGen Generate overlapping peptides for any protein
• Hepitope Search for hopeful epitopes based on HLA enrichment
• HLA Frequency Analysis Tools Calculate HLA frequencies or HLA linkage disequilibrium in a population
• ELF Epitope location finder
• Motif Scan Scan alignments for HLA binding motifs
• PrimAlign Align nucleotide sequences against our alignments
• HIV/SIV Sequence Locator Tool (formerly HXB2 Numbering Engine)
• SeqPublish Produce pretty alignments for publication
• BLAST Search sequences against our annotated HIV sequences
• ODprep/ODfit Calculate antibody titers based on concentration and optical density data
• Mosaic Generate candidate vaccine protein cocktails
  • Epicover Epitope coverage assessment tool
  • Posicover Positional epitope coverage assessment tool

• All Tools List of all software and tools in both the HIV Sequence and Immunology Databases

External Tools

• BIMAS HLA Peptide Binding Predictions
• The SYFPEITHI Database MHC ligands, peptide motifs and epitope prediction
• NetChop Neural network predictions for cleavage sites of the human proteasome
• JenPep Peptide binding database
• NetMHCpan Quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence

HIV Vaccine Studies and Related Databases

• IAVI Database of Preventive AIDS Vaccines in Human Trials
• Database of HIV Vaccines in Development from The Pipeline Project
• NIH AIDSinfo HIV/AIDS Vaccines
• LANL HIV/SIV Vaccine Trials Database

Immunology Related Links

• IMGT, The International Immunogenetics Database
• NIH AIDS Research and Reference Program HIV immunology reagents
• Antibody Resource
• Immunology Link site
• NIBSC, Centralised Facility for AIDS Reagents
• dbMHC The MHC database at NCBI
• HLA Informatics Group-Anthony Nolan Bone Marrow Trust
• Molecular Immunolgy Foundation
• Allele Project Allele frequencies in worldwide populations
• Immune Epitope Database (IEDB)
• Immunopaedia A site designed to help close the gap between clinical observations and immunology knowledge

HIV/AIDS Links

• HIV/AIDS Links List of many HIV/AIDS-related links maintained by the HIV Sequence Database

Last modified: Tue Mar 25 13:24:24 MDT 2008