HLAgazeteer: Functional and Organizational Categories of Genes Supported...

In HLAtools: Toolkit for HLA Immunogenomics

Functional and Organizational Categories of Genes Supported by the IPD-IMGT/HLA Database

Description

A list object of nineteen vectors that identify genes in the HLA region that share specific commonalities. This object is built by the buildGazeteer() function.

Usage

data(HLAgazeteer)

Format

A large list of 19 vectors that define specific categories of genes supported by the IPD-IMGT/HLA Database

.

• (align: all genes with alignments in the IPD/IMGT-HLA GitHub Repository)

• (gen: genes with genomic alignments in the IPD/IMGT-HLA GitHub Repository)

• (nuc: genes with nucleotide alignments in the IPD/IMGT-HLA GitHub Repository)

• (prot: genes with protein alignments in the IPD/IMGT-HLA GitHub Repository)

• (nogen: genes with no genomic alignments)

• (nonuc: genes with no nucleotide alignments)

• (noprot: genes with no protein alignments)

• (pseudo: pseudogenes)

• (frag: gene fragments)

• (hla: HLA genes)

• (expressed: genes that are expressed)

• (notexpressed: genes that are not expressed)

• (classireg: genes found in the HLA class I region)

• (classihla: class I HLA genes)

• (classiireg: genes found in the HLA class II region)

• (classiihla: class II HLA genes)

• (classical: classical HLA genes)

• (nonclassical: non-classical HLA genes)

• (map: all genes organized by 5' to 3' map order on the genomic reference + strand)

• (version: IPD-IMGT/HLA Database version used to build the HLAgazeteer)

Source

https://hla.alleles.org/genes

https://github.com/ANHIG/IMGTHLA/tree/Latest/alignments

Andersson Front. Biosci. 1998, 3(4), 739–745. https://doi.org/10.2741/a317

Alexandrov et al. HLA 2023, Vol.102(5), p.599-606. https://doi.org/10.1111/tan.15180

https://www.ncbi.nlm.nih.gov/nucleotide/NC_000009.12

HLAtools documentation built on June 8, 2025, 12:24 p.m.