HIV molecular immunology database

 

HIV Immunology Database FAQ

 

Site overview

What can I find on this website?

The HIV immunology database is a repository of information about HIV epitopes and antibody binding sites, plus associated tools. For more information, see About the Immunology Database.

Who are you?

The database staff includes immunologists, molecular biologists, sequence analysts, computer technicians, post-docs, and graduate research assistants. We are part of the Theoretical Biology and Biophysics Group (T-6) at the Los Alamos National Laboratory. We are funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases through an interagency agreement with the Department of Energy. We are advised by a group of external database editors.

Why are there several separate databases here?

Our databases are organized around several areas of virus research. The links on the menu will take you to the other areas of this site. In particular, this immunology database is closely tied to the HIV Sequence Database.

I am HIV-positive. Does this site contain information useful to me?

The information on this site assists researchers who study the AIDS virus and are seeking ways of defeating it. The information available here is not directly helpful to patients. We are not qualified to give medical advice of any kind. You can find links to websites with information about AIDS in the HIV Sequence Database Links.

 

Tools

I want to use one of your tools. What format should my data be in?

Most tools provide a Help file with information about the data type(s) accepted. In general, data and sequences should be in appropriate text file formats, not in Word (.doc) or other word processing formats. Sequences are accepted in a variety of common formats. If you need help, contact us.

I am having a problem using one of your tools. Can you help?

Yes, we can help troubleshoot the problem, and your problem may help us improve our tools. Please write to immuno@lanl.gov; include your input file(s) if possible.

 

How do I search for epitopes?

You can search for epitopes based on a number of criteria: genome region, epitope sequence, author name(s), etc. We also provide maps and tables. For more information about searches, see Search Help.

Can I search for a CTL epitope based on its common name, such as "RY11"?

Yes, but be careful. Names like RY11 are not specific - there may be multiple RY11's. Furthermore, the results will not include every entry for RY11, as some authors don't use these names. We recommend searching for the common name only as a way to find the full epitope sequence (or its coordinates), and then using this information to do the search.

In the epitope tables, what do you mean by "A list", "B list" or "best-defined" CTL epitopes?

The "A list" is a nickname for the "Best-defined" epitopes. The list of Best-defined epitopes is revised yearly by Christian Brander and colleagues. This list includes only those HIV-1 epitopes that are optimal and well-substantiated.

In contrast, the CTL "B list" is the summary table of all CTL epitopes in our database.

I am looking at epitopes in the Epitope Maps. When I use your search interface to search for an epitope sequence from the map, I don't obtain all of the epitopes displayed at that map location. Why?

Not all epitopes from a specific map location share exactly the same amino acid sequence. The sequence shown on the map is the B-clade reference sequence HXB2; the epitopes shown may have come from another strain of HIV and thus have a different sequence. The next question addresses how to obtain details for all epitopes that appear on the map.

You have epitope data in three forms: search results, maps, and tables. Will I find exactly the same data in all three?

The maps and tables are based on exactly the same data. They contain the vast majority of the data currently available through the search interface. There may a few newly-entered epitopes available through the search interface that are not yet in the maps and tables.

Where can I find information about CTL variants and escape mutants?

We provide a search interface and table of Epitope Variants and Escape Mutations.

Do you have data on HIV-2 and SIV epitopes?

The focus of this database is HIV-1. Some HIV-2 epitopes are included in our searches, maps and tables. SIV epitope data are not incorporated into our searchable databases. We provide a table of SIV epitopes, based on a 2006 review article (PDF): Beyond Mamu-A*01+ Indian Rhesus Macaques: Continued Discovery of New MHC Class I Molecules that Bind Epitopes from the Simian AIDS Viruses, by Loffredo et al. 2006.

 

Antibody searches

How can I find information on antibodies to HIV-1?

You can search for antibodies based on a number of criteria: genome region, epitope sequence, author name(s), etc. For more information about antibody searches, see Search Help.

We also provide:

Why does the output page from the Antibody Search look different than the output from the CTL or Helper Search?

The antibody database is structured differently. While the CTL and helper databases have a separate database entry for each reference, the antibody database has a single entry for each antibody, often with many references.

When I search for an antibody I get a huge list of notes. How can I find just the notes that I need?

You can limit the number of notes by including an author name, keyword, or note text, and selecting the option to show only the notes related to your selection.

I want to obtain an antibody that is described in your Antibody Database. Can you tell me where to obtain it?

Some of our older database entries include contact information for the person who originally described the antibody. Searching for the antibody name and the keyword "antibody generation" should lead to the note for the original reference. You can also try a web search engine to find commercial or other sources.

 

HIV molecular biology

What is HXB2? Where can I get a copy of this sequence?

HXB2 is a subtype B HIV-1 isolate used in all our databases as the reference strain for aligning and numbering HIV-1 sequences. The actual sequence (either DNA or protein) can be obtained from any of our premade HIV-1 Alignments, Sequence Locator tool, or from the Sequence Search Interface.

How can I determine the coordinate position of my epitope?

Just put your epitope sequence into Sequence Locator.

What are HIV "subtypes"? What does CRF01 mean?

In the sequence database, we have informational web pages that describe the subtypes (clades) of HIV. Subtypes are usually indicated by a letter (A, B, C, etc.). HIV also has circulating recombinant forms (CRFs), which are recombinants of two or more subtypes. For more information, see Overview of Subtypes and HIV Nomenclature.

Where can I find more information about the HIV virus, such as a map of the genome or a list of the sizes and breakpoints of the genes and proteins?

The HIV Sequence Database provides detailed information in many formats. In particular, see HIV-1 Gene Map and Tutorials.

HIV-1 gene map

How can I align epitopes to reference sequences?

From the CTL, Helper, or Antibody search results, click the link marked "Epitope Alignment" to see that specific epitope aligned to a large set of sequences from the sequence database. In addition, we provide premade Epitope Alignments, which show all epitopes aligned to subtype reference sequences. The QuickAlign tool provides additional options.

Why does p15 (RNase) not appear in your epitope maps and tables?

HIV-1 p15 is a domain within the heterodimeric reverse transcriptase (RT) enzyme. It is included as part of RT.

 

Annotation

How are the data in the HIV Molecular Immunology database entered? How reliable is the information?

Members of our staff review published articles and enter the information manually. We strive for accuracy, and we have several quality assurance mechanisms. Nonetheless, we are human, and occasional errors occur. Before using the information presented here, confirm it by reading the original reference(s).

How often are new data entered?

New data are entered into the searchable databases almost daily. New data are entered into the maps and tables approximately weekly. The current database statistics (total numbers of database entries) are shown on the About the Immunology Database page; these statistics are updated daily.

How are keywords assigned?

Keywords are chosen as each published paper is entered. The keywords are used by our database in ways that we have found useful, not necessary as used by the authors of the paper. If you have any questions about how we use particular keywords, please contact us.

How do you decide whether to report 2-digit or 4-digit HLA types associated with an epitope?

In general, we enter the HLA as it is provided in the original publication.

I found a mistake in your database. Will you fix it?

Yes! Please write to immuno@lanl.gov. We will be happy to look into it and correct it if necessary.

 

Additional information and resources

Where can I find which genotypes (4-digit HLAs) are included in a particular serotype or supertype?

We present this information in three forms: HLA Dictionary, Binding Motif Dictionary, and Supertype Dictionary.

Do you have a database of binding motifs for human HLA types?

We provide such a database as part of the Motifscan tool. The data are presented as tables in both the Binding Motif Dictionary and Supertype Dictionary. Binding motif information is also provided by the ELF tool, along with binding predictions.

Do you have a database of reactive peptide sequences from patients of known HLA types?

We currently have several large sets of this type of data that you can search. See HLATEM.

Do you have HIV sequences from patients of known HLA types?

The HIV Sequence Database contains many sequences from patients of known HLA types. Using the Sequence Search Interface, click on "Patient Information" and check the box labeled "Only sequences with HLA information". Sequences may be downloaded as DNA or as protein(s).

My question isn't answered here, can you help me?

Yes, please write to immuno@lanl.gov. If you do not receive an answer within 3 business days, please write again. We try to answer every inquiry promptly, but occasionally one is missed. For questions related to the LANL Sequence Database, see HIV Sequence Database FAQ.

 

Questions or comments? Contact us at immuno@lanl.gov
 
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