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HIV Sequence Database



Tutorials and Basic Information

 

How to Use These Databases

Sequence Database Workshop (YouTube)
Sequence database slides (4.5 MB PDF) from 2022 Keystone conference

Immunology Database Workshop (YouTube)
Immunology database slides (9 MB PDF) from 2022 Keystone conference

More HIV Database presentations from conference workshops

Tutorials

Sequence quality control YouTube video tutorial about using our QC tool to find common problems in newly-obtained HIV sequences

Sequence quality control written tutorial about common problems with sets of viral sequences

How to make a phylogenetic tree written tutorial on tree building

FAQs

FAQs about the HIV Sequence Database

FAQs about the HIV Immunology Database

Articles

Stalking the AIDS Virus [PDF] article from 2003 LANL Research Quarterly about HIV Database research on the HIV-immune system interaction as a step toward an AIDS vaccine

Reference Information

Circulating recombinant forms (CRFs) gives details about all documented CRFs of HIV-1

HIV-1 gene map illustrates the genes/proteins of HIV-1, including HXB2 breakpoints

HXB2 annotated spreadsheet (.xls) provides a fully-annotated sequence of HXB2 with base-by-base detail

HIV and SIV subtype nomenclature gives an overview of HIV and SIV subtype nomenclature, particularly HIV-1 groups and subtypes

Primate immunodeficiency virus nomenclature lists SIV species and nomenclature

How the HIV database classifies sequences explains how recombinants are named and annotated

Common sequence formats for alignments shows examples of common sequence formats for alignments

How to cite this Database explains how to cite this website and the printed HIV compendia

Codes and symbols in sequences decodes the symbols and IUPAC codes that appear in sequences and alignments

Codon table gives the translation of nucleotides into amino acids

HIV numbering relative to reference strain HXB2

SIV numbering relative to reference strain SIVmm239

Links HIV/AIDS resources and bioinformatics tools on other websites

 

last modified: Wed Aug 16 14:39 2023


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