Variants Database Help

Description

The variants database contains information about sequence variants and mutations of HIV-1 CTL epitopes. Only variants tested for immunological response are included. Variants are usually omitted if the paper only provides sequence or statistical data.

For general information about the HIV Immunology databases and searches, see HIV Immunology Search Help.

Variants Search & Results Fields

This is a brief description of the database fields in the variant search and results pages.

HIV protein

The protein for which the epitope was defined. When an epitope spans two proteins that we treat separately in the database, such as p17-p24, both are indicated.

HXB2 location

The HXB2 protein coordinates within the protein selected in the "HIV protein" field above.
Three options determine the type of search:

1. Results overlap with query location: finds epitopes that overlap any residue of the specified location. To find epitopes that contain a single specific residue, you can enter the same coordinate number in both boxes.
2. Results contained within query location: finds epitopes that are contained within the specified range. Results will be the same length or shorter than the query.
3. Results exact match to query location: finds epitopes that have exactly the specified start and stop coordinates.

Epitope or Variant Sequence

The amino acid sequence of the epitope or variant.
Three options determine the type of search:

1. Results contain query sequence: finds epitopes that contain the query sequence. Results will be the same length or longer than the query.
2. Results exact match to query sequence: finds epitopes with the exact coordinates and exact sequence as the query.
3. Results fuzzy match to query sequence: finds epitopes with the exact coordinates as the query, but with up to 25% difference in the amino acid sequence.

Record number

A unique number assigned to an epitope by the database. Please refer to this number if you have any comments or questions about an entry.

Variant record number

A unique number assigned to a variant by the database. Please refer to this number if you have any comments or questions about an entry.

Mutation Type

Mutations are classified into various types, depending on the evidence presented in the paper. Assigning the mutation type is sometimes a subjective judgement of the annotator; it is not always clear in the paper. Read the Notes for the variant carefully, and refer to the original paper if necessary.
See: List of Variant and Mutation Types

MHC/HLA

The MHC (or HLA) presenting molecules as described by the primary authors.

Method

The method(s) used to ascertain the type of mutant.

Notes

In the notes for the variant, the annotator explains the evidence for assigning the mutation type.