- Tools specific for HIV/SIV
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General use tools with some HIV/SIV-specific features
- General use tools
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All Tools List
of all software and tools in both the HIV
sequence and immunology databases
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BIMAS HLA Peptide Binding Predictions
Ranks potential n-mer peptides based on a predicted half-time of
dissociation to HLA class I molecules
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SYFPEITHI Epitope Prediction
Predicts the binding of a given amino acid sequence to a defined
HLA type
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PAProC Predicts cleavages by
human and yeast 20S proteasomes
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PREDEP
MHC class I epitope prediction
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MHCPred
Predicts MHC/peptide or TAP/peptide IC50 binding values
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Immune Epitope Database (IEDB)
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DTU Heathtech (Formerly: Center for Biological Sequence Analysis)
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NetMHC
Predicts MHC binding ability of peptides
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NetMHCpan
Predictions of peptide binding to any HLA-A and -B locus
protein of known sequence
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NetChop
Predicts cleavage sites of the human proteasome
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NetCTL
Predicts CTL epitopes by combining MHC supertype binding, TAP
binding, and proteasome cleavage scores
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IMTech
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CTLPred
Prediction of CTL epitopes, combining MHC binding, TAP
binding, and cleavage
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MHC2Pred
Prediction of promiscuous MHC class II binders
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MMBPred
Prediction of promiscuous MHC class I binders and
mutations that allow high-affinity binding
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Pcleavage
Predicted proteasome or immunoproteasome cleavage
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ProPred
Predicted MHC class II-peptide binding
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ProPred-I
Predicted MHC class I-peptide binding; optional proteasome
cleavage filter
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TAPPred
Prediction of binding affinity of TAP proteins
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MHCBN 4.0
MHC-peptide binders and nonbinders, TAP-peptide binders and
nonbinders, and T-cell epitopes
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NEP Server Neutralization-based Epitope Prediction
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
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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)
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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)
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iHMMune
Immunoinformatics web site and methods developed in the laboratory
of Dr. Andrew Collins at the University of New South Wales, Sydney
Australia:
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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.
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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)
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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)
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HTJoinsolver An programming method that uses conserved immunoglobulin gene motifs to improve performance of aligning V-segments of rearranged immunoglobulin genes.
(Reference: Russ et al. HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs.
BMC Bioinformatics May 23;16(1):170 (2015)
PMID 26001675)
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IgDiscover IgDiscover analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes).
(Reference: Corcoran, Martin M. and Phad, Ganesh E. and Bernat, Néstor Vázquez and Stahl-Hennig, Christiane and Sumida, Noriyuki and Persson, Mats A.A. and Martin, Marcel and Karlsson Hedestam, Gunilla B.
Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.
Nature Communications 7:13642 (2016).
PMID 27995928)
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HIV/AIDS Links
HIV/AIDS-related links maintained by the HIV
Sequence Database