HIV Molecular Immunology Database: Tools & Links

Tools Produced by the Los Alamos HIV Databases

• CATNAP: Compile, Analyze and Tally NAb Panels Download or analyze neutralization data
• CombiNAber Predict the neutralization of combinations of antibodies
• HIV Genome Browser Display HIV genome and proteome
• QuickAlign Align amino acids or nucleotides against our alignments
• Analyze Align Show weblogos, calculate frequency by position, and find variants in an alignment
• Alignment Slicer Cut vertical slices from sequence alignments
• PeptGen Generate overlapping peptides for any protein
• PepMap Generate peptide maps in Fasta, HTML and PDF formats
• Motif Scan Scan alignments for HLA binding motifs
  • HLA genotype/serotype dictionary
  • HLA genotype/motif dictionary
  • HLA supertype dictionaries
• 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
• Sequence Locator Tool Find the location of any HIV/SIV sequence
• SeqPublish Produce pretty alignments for publication
• Heatmap Display a table of numbers using colors to represent the numerical values
• Epigraph Vaccine Suite Design and assess Epigraphs for vaccine design
• Mosaic Vaccine Suite Design and assess polyvalent protein sequences for T-cell vaccines
• N-Glycosite Find N-linked glycosylation sites
• Highlighter Highlight matches and mismatches in a set of aligned sequences
• Protein Feature Accent View 3D graphics of HIV proteins
• Variable Region Characteristics analyzes Env variable loops and reports length, glycosolations, and net charge

• All Tools List of all software and tools in both the HIV sequence and immunology databases

External Tools for Epitope Prediction

• BIMAS HLA Peptide Binding Predictions Ranks potential n-mer peptides based on a predicted half-time of dissociation to HLA class I molecules
• SYFPEITHI Epitope Prediction Predicts the binding of a given amino acid sequence to a defined HLA type
• PAProC Predicts cleavages by human and yeast 20S proteasomes
• PREDEP MHC class I epitope prediction
• MHCPred Predicts MHC/peptide or TAP/peptide IC₅₀ binding values
• Microsoft Research Epitope Predictor Computes the probability that a given n-mer is a T-cell epitope restricted to a given HLA allele
• Max Planck Institute
  • FRAGPredict Prediction of proteasome cleavage
  • MAPPP Prediction of MHC-I antigenic peptide processing
• Immune Epitope Database (IEDB)
  • MHC Class I Binding
  • MHC Class II Binding
  • NetChop and NetCTL Predictors of proteasomal processing and T cell epitopes
  • MHC Processing Predictions Combines predictors of proteasomal processing, TAP transport, and MHC binding to produce an overall score for each peptide's intrinsic potential of being a T-cell epitope
• Center for Biological Sequence Analysis (CBS)
  • NetMHC Predicts MHC binding ability of peptides
  • NetMHCpan Predictions of peptide binding to any HLA-A and -B locus protein of known sequence
  • NetChop Predicts cleavage sites of the human proteasome
  • NetCTL Predicts CTL epitopes by combining MHC supertype binding, TAP binding, and proteasome cleavage scores
  • HLArestrictor Given a peptide sequence and the HLA type of an individual, predicts all 8-11mer peptide binders and minimal epitopes
• IMTech
  • CTLPred Prediction of CTL epitopes, combining MHC binding, TAP binding, and cleavage
  • MHC2Pred Prediction of promiscuous MHC class II binders
  • MMBPred Prediction of promiscuous MHC class I binders and mutations that allow high-affinity binding
  • Pcleavage Predicted proteasome or immunoproteasome cleavage
  • ProPred Predicted MHC class II-peptide binding
  • ProPred-I Predicted MHC class I-peptide binding; optional proteasome cleavage filter
  • TAPPred Prediction of binding affinity of TAP proteins
  • MHCBN 4.0 MHC-peptide binders and nonbinders, TAP-peptide binders and nonbinders, and T-cell epitopes
• NEP Server Neutralization-based Epitope Prediction

External Tools for Germline Antibody Reconstruction

For an informative review and applied example of statistical approaches to reconstruction of B cell clonal lineages undergoing affinity maturation, see: Kepler TB. Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors. F1000Res. 2013 Apr 3;2:103. PMID 24555054

• IgBlast This tool was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences and also T cell receptor (TR) sequences. It reports the germline V, D and J gene matches to the query sequences, annotates the immunoglobulin domains (FR1 through FR3), identifies V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions, and indicates whether the rearrangement is in-frame or out-of-frame.
  (Reference: Ye J, Ma N, Madden TL, Ostell JM (2013) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Research 41: W34-W40 PMID: 23671333)
• Cloanalyst Cloanalyst is the software implementation of the most recent suite of statistical methods for the inference of antigen receptor rearrangements and other analyses useful in the study of antibody somatic genetics from the laboratory of Dr. Thomas Kepler, of Boston University. Cloanalyst performs a Bayesian analysis of antibody genes to compute posterior probabilities over rearrangement parameters and unmutated ancestral rearrangements, using either single immunoglobulin polynucleotide sequences or sets of clonally related immunoglobulin sequences. (Manuscript in preparation)
• iHMMune Immunoinformatics web site and methods developed in the laboratory of Dr. Andrew Collins at the University of New South Wales, Sydney Australia:
  • iHMMune-align uses hidden Markov model-based alignments to align rearranged immunogolobulin sequences. It described as "an alignment tool designed specifically for modeling the antibody generation process and identifying the constituent germline genes of a human heavy chain mature variable region sequence". The input is full-length or nearly full length genes with VDJ rearrangements.
  • Short iHMMune-align is a version of this code that takes short sequences using the BIOMEDs primers.
  (Reference: Gaëta BA, Malming HR, Jackson KJ, Bain ME, Wilson P, Collins AM. iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics. 2007 Jul 1;23(13):1580-7. PMID 17463026)
• IMGT/V-Quest The international ImMunoGeneTic information system, which supplies global references and access to sequence, genomic, and structural immunological data. IMGT/V-QUEST identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. It enables analysis of human and some non-human primates and other animals. IMGT/V-QUEST identifies the V-REGION mutations relative to the closest germline V gene, and detects insertions and deletions in the submitted sequences by reference to IMGT numbering. It can also be used to identify T-cell receptors.
  (References: Brochet X, Lefranc MP, Giudicelli V. IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 2008 Jul 1;36:W503-8. PMID 18503082
  Giudicelli V, Brochet X, and Lefranc M.-P. IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences Cold Spring Harb Protoc. 2011 Jun 1;2011(6). PMID 21632778)
• Joinsolver This website is maintained by the NIH/NIAID, and provides analysis of human immunoglobulin CDR3 region VDJ recombination and comparison to germline genes, and it also searches for P and N type additions to the VHD and DJH junctions. It also contains germline databases with Kabat or IMGT numbering.
  (Reference: Souto-Carneiro MM, Longo NS, Russ DE, Sun H, and Lipsky PE. Characterization of the human immunoglobulin heavy chain antigen binding complementarity determining region 3 using a newly-developed software algorithm, JOINSOLVER. 2004 J. Immunol. 172 (11):6790-6802. PMID 15153497)

External Immunology Databases and Tools

• The SYFPEITHI Database MHC ligands, peptide motifs and epitope prediction
• Immune Epitope Database (IEDB) Databases of HIV and HCV epitopes
• dbMHC MHC database at NCBI
• HLA Nomenclature home page
  • Nomenclature for Factors of the HLA System Update to HLA Nomenclature, 2009
  • The IMGT/HLA Dictionary at EBI
  • International Immunogenetics Database (IMGT) Aligned and annotated HLA sequences
  • EMBL-IMGT HLA Allele Query Form Aligned and annotated T-cell receptor sequences nomenclature
• MHC Haplotype Project Haplotypes of MHC-linked diseases, with complete genomic sequences, variations (SNPs and DIPs), and ancestral relationships
• HCV Immunology Database HCV epitopes
• RCSB Protein Data Bank (PDB) Structural database and viewing tools, MHC/peptide/TCR combinations
• IMGT/HLA Database
• Neutralization Panel Analysis Tool and Antibody Database Computational tool to identify Env residues critical for antibody activity (West et al. 2013). The tool analyses and organizes HIV-1 neutralization data from studies with large neutralization panels, together with viral and antibody sequences and structural information. The tool is available from the authors upon request.
• HIV Mutation Database A database of mutagenesis and mutation information on HIV collated from the scientific literature using computational text-mining.

HIV Vaccine Studies and Related Databases

• AIDSinfo database of HIV/AIDS Vaccines
• LANL HIV/SIV Vaccine Trials Database

Other Immunology Links

• NIH AIDS Research and Reference Program HIV immunology reagents
• CHAVI HIV/AIDS reagents
• Antibody Resource
• Immunology Link site
• NIBSC, Centralised Facility for AIDS Reagents
• Molecular Immunology Foundation
• Allele Project Allele frequencies in worldwide populations
• 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