HIV Database Tools
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Analysis and Quality Control
Entropy quantifies positional variation in an alignment using Shannon Entropy HIV BLAST finds sequences similar to yours in the HIV database Hypermut detects hypermutation jpHMM at GOBICS detects subtype recombination in HIV-1; hosted at GOBICS as a collaboration between the Department of Bioinformatics, University of Göttingen and the Los Alamos HIV Sequence Database N-Glycosite finds potential N-linked glycosylation sites PCOORD multidimensional analysis of sequence variation Quality Control runs several tools to allow quick QC analysis of HIV-1 sequences; optional step prepares sequence submission for GenBank RIP (Recombinant Identification Program) detects HIV-1 subtypes and recombination SNAP calculates synonymous/non-synonymous substitution rates SUDI Subtyping plots the distance of your sequence to established subtypes VESPA (Viral Epidemiology Signature Pattern Analysis) detects residues with different frequencies in two sequence sets Alignment and sequence manipulation
Codon Alignment takes a nucleotide alignment and returns a codon alignment and translation Consensus Maker computes a customizable consensus ElimDupes compares the sequences within an alignment and eliminates any duplicates Gap Strip/Squeeze removes columns with more than a given % of gaps Gene Cutter clips genes from a nucleotide alignment, codon-aligns, and translates HIValign uses our HMM alignment models to align your sequences PepMap can be used to map epitopes, functional domains, or any protein region of interest Pixel generates a PNG image of an alignment using 1 or more colored pixel(s) for each residue QuickAlign (formerly Epilign and Primalign) aligns a nucleotide or protein sequence (e.g., primer or epitope) to the appropriate genome alignment Sequence Locator finds the standard numbering of your HIV or SIV nucleotide or protein sequence SynchAlign aligns overlapping alignments to one another Translate nucleotide sequences to 1-letter amino acids Format and display
Format Converter converts between alignment formats Highlighter highlights mismatches, matches, transitions and transversion mutations and silent and non-silent mutations in an alignment of nucleotide sequences Protein Feature Accent provides an interactive 3-D graphic of HIV proteins; can map a sequence feature (a short functional domain, epitope, or amino acid) and see it spatially Protein Structure provides a visualization tool for protein sequence properties Recombinant HIV-1 Drawing Tool creates a graphical representation of your HIV-1 intersubtype recombinant SeqPublish makes publication-ready alignments |
Phylogenetics
Branchlength calculates branch lengths between internal and end nodes FindModel finds which evolutionary model best fits your sequences PhyloPlace reports phylogenetic relatedness of an HIV-1 sequence with reference sequences PhyML generates much better trees than our simple TreeMaker tool Poisson-Fitter estimates time since MRCA and star-phylogeny. For use with acute (low diversity) samples. Rainbow Tree Color code phylogenetic tree branches according to labels in the sequence names TreeMaker generates a quick-and-dirty phylogenetic tree TreeRate finds the phylogenetic root of a tree and calculates evolutionary rate Immunology
ELF (Epitope Location Finder) identifies known and potential epitopes within peptides Epilign (QuickAlign) aligns a protein sequence (e.g., epitope) to the appropriate protein alignment Heatmap displays a table of numbers by using colors to represent the numerical values Hepitope identifies potential epitopes based on HLA frequencies Mosaic Vaccine Tool Suite designs and assesses polyvalent protein sequences for T-cell vaccines Motif Scan finds HLA anchor motifs in protein sequences for specified HLA serotypes, genotypes or supertypes PeptGen generates overlapping peptides from a protein sequence Database search interfaces
ADRA Antiviral Drug Resistance Analysis, a resistance mutation database Advanced Search creates a custom search interface Antibodies search for HIV antibodies by protein, immunogen, AB type, isotype, author, keywords CTL/CD8+ Search searches for CD8+ epitopes by protein, immunogen, HLA, author, keywords Geography shows the geographic distribution of sequences in the database Intra-patient Search retrieves intra-patient sequence sets Sequence Search searches for sequences based on numerous criteria T-Helper/CD4+ Search search for CD4+ epitopes by protein, immunogen, HLA, author, keywords Vaccine Trials Database finds past vaccine trials and their results Additional Resources
External tools tools and programs on other websites |