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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 for quick troubleshooting 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

Variable Region Characteristics characterizes features within a peptide excised from a protein alignment, summarizing and reporting the following peptide characteristics: length, number of N-linked glycosylation sites. It is particularly useful for characterizing hypervariable regions in Env.

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

Alignment and sequence manipulation

Alignment Slicer cuts vertical slices from sequence alignments

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

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

HIV 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

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; now included in the TreeRate tool

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 branch lengths and 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

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

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

Reference Sequence Coordinate Search retrieves HXB2 and Mac239 features and coordinates

Intra-patient Search retrieves intra-patient sequence sets

Neutralizing Antibody Contexts and Features retrieves information about neutralizing antibodies

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 Apr 10 13:58 2014


Questions or comments? Contact us at seq-info@lanl.gov.

 
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