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HIV sequence database

HIV Database Tools

Tools specific for HIV/SIV
General use tools with some HIV/SIV-specific features
General use tools
Analysis and Quality Control

Entropy quantifies positional variation in an alignment using Shannon Entropy

GenSig identifies genetic signatures. It can work on any phenotype file given in conjunction with a codon-aligned nucleotidealignment of a protein coding region

Glycan Shield Mapping shows mapping absent hole-causing potential N-linked glycosylation sites (PNGS) on predicted glycan shields for an ENV sequence

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 for quick troubleshooting of HIV-1 sequences; optional step prepares sequence submission for GenBank

RAPR (Recombinant Analysis PRogram) uses the Wald-Wolfowitz Runs Test to check for recombination in every triplet in the alignment.

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

Variable Region Characteristics summarizes features of peptides from a protein alignment, reporting peptide characteristics such as length and N-linked glycosylation sites; particularly useful for characterizing variable regions of Env

VESPA (Viral Epidemiology Signature Pattern Analysis) detects residues with different frequencies in two sequence sets

Alignment and sequence manipulation

Align Multi-tool manipulates sequence alignments, including sorting, pruning, and renaming

Alignment Slicer cuts vertical slices from sequence alignments

Analyze Align shows weblogos, calculates frequency by position, and finds variants in an alignment

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 short nucleotide or protein sequences (e.g., primers, epitopes) to our prebuilt genome or protein alignments, or to a user 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

GenBank Entry Generation produces GenBank Sequin files for HIV-1, HIV-2, and SIV sequences, plus associated metadata

Genome Browser uses jBrowse to display diverse data about the HIV-1 genome and proteome

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

Recombinant HIV-1 Drawing Tool creates a graphical representation of your HIV-1 intersubtype recombinant

SeqPublish makes publication-ready alignments


AnnotateTree creates a colored and weighted phylogenetic tree

Branchlength calculates branch lengths between internal and end nodes; now included in the TreeRate tool

FindModel finds which evolutionary model best fits your sequences

IQ-TREE is a fast and effective stochastic algorithm for finding Maximum Likelihood trees, including site-specific rates of evolution at each alignment position

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 Neighbor Joining phylogenetic tree

TreeRate finds the phylogenetic root of a tree and calculates branch lengths and evolutionary rate


CATNAP (Compile, Analyze, Tally NAb Panels) provides meta-analysis of published neutralization panel data

CombiNAber predicts and analyzes combination antibody neutralization scores using IC50 and/or IC80 for individual antibodies

ELF (Epitope Location Finder) identifies known and potential epitopes within peptides

Epigraph Tool Suite uses input of diverse sequences to generate Epigraph sequences for use in vaccine or reagent design

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

Neutralization Index computes a tier-like score for sera (using ID50 titers) or antibodies (using IC50 titers)

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

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

Reference Sequence Coordinate Search retrieves HXB2 and Mac239 features and coordinates

Intra-patient Search retrieves intra-patient sequence sets

Neutralizing Antibody Contacts and Features retrieves neutralizing antibody contact sites and other HIV-1 Env features

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



last modified: Thu Nov 12 11:03 2020

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