HIV Database Tools
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Analysis and Quality Control
HIV BLAST finds sequences similar to yours in the HIV database VESPA (Viral Epidemiology Signature Pattern Analysis) detects residues with different frequencies in two sequence sets PCOORD multidimensional analysis of sequence variation N-Glycosite finds potential N-linked glycosylation sites Entropy quantifies positional variation in an alignment using Shannon Entropy SNAP calculates synonymous/non-synonymous substitution rates RIP 3.0 (Recombinant Identification Program) detects HIV-1 subtypes and recombination SUDI (SUbtyping DIstance) plots the distance of your sequence to established subtypes Hypermut detects hypermutation jpHMM (jumping profile Hidden Markov Model) compares a sequence to an alignment; hosted at GOBICS as a collaborative effort between the Department of Bioinformatics of the University of Göttingen and the Los Alamos HIV Sequence Database Group; used to detect recombination in HIV-1. Alignment and sequence manipulation
Sequence Locator finds the standard numbering of your HIV or SIV nucleotide or protein sequence Translate nucleotide sequences to 1-letter amino acids Gapstreeze removes columns with more than a given % of gaps Consensus Maker computes a customizable consensus Gene Cutter clips genes from a nucleotide alignment, codon-aligns, and translates SynchAlign aligns overlapping alignments to one another Primalign aligns a nucleotide sequence (e.g., primer) to the complete genome alignment Epilign aligns a protein sequence (e.g., epitope) to the appropriate protein alignment EpimDupes removes duplicate sequences from an alignment Format and display
Protein Feature Accent provides an interactive 3-D graphic of HIV proteins; the user can map a sequence feature (a short functional domain, epitope, or amino acid) and see where it occurs spatially Format Converter converts between alignment formats SeqPublish makes publication-ready alignments Highlighter highlights mismatches, matches, transitions and transversion mutations and silent and non-silent mutations in an alignment of nucleotide sequences Recombinant Drawing Tool creates a graphical representation of your HIV-1 subtype recombinant Protein Structure Analysis provides a visualization tool for protein sequence properties |
Phylogenetics
TreeMaker generates a quick-and-dirty phylogenetic tree FindModel finds which evolutionary model best fits your sequences Branchlength calculates branch lengths between internal and end nodes Immunology
Mosaic Vaccine Tool Suite Design and assess polyvalent protein sequences for T-cell vaccines PeptGen generates overlapping peptides from a protein sequence ELF (Epitope Location Finder) identifies known and potential epitopes within peptides MotifScan finds HLA anchor motifs in protein sequences for specified HLA serotypes, genotypes or supertypes Hepitope identifies potential epitopes based on HLA frequencies Epilign aligns a protein sequence (e.g., epitope) to the appropriate protein alignment Heatmap displayes a table of numbers by using colors to represent the numerical values. Database search interfaces
Sequence search searches for sequences based on numerous criteria Advanced search creates a custom search interface Geography geographic distribution of sequences in the HIV database CTL epitopes searches for CD8 epitopes by protein, immunogen, HLA, author, keywords T helper epitopes search for CD4 epitopes by protein, immunogen, HLA, author, keywords Antibodies search for HIV antibodies by protein, immunogen, AB type, isotype, author, keywords Vaccine trials database the vaccine trials database for past trials and their results ADRA Resistance mutation database: search for mutations related to drug resistance Other tools
HDent and HDdist perform analysis of heteroduplex mobility shifts ODprep and ODfit calculate antibody titers based on concentration and optical density data External tools
External tools lists tools and programs on other websites |