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Tutorials
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I. Architecture of HLAsupE |
II. Definition of HLA supertypes |
III. Usage of HLAsupE |
i. Search for HLA supertype-specific epitopes or peptides |
ii. Map HLA supertype-specific epitopes or peptides on an input protein sequence |
iii. Search for mutated analogues of an input peptide |
iv. Search for the promiscuous peptides presented by HLA molecules across supertypes |
IV. Notes |
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Architecture of HLAsupE
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Definition of HLA supertypes in HLAsupE
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The HLA class I supertypes for the HLA-A and B loci used here were defined by Sidney et al (2008), and the supertypes used for the HLA-C loci were based on the classification presented by Doytchinova (2004). The HLA class II supertypes used were consistent with Doytchinova’s definition (2005). Due to the relatively low number of HLA-DPA and DPB alleles with available peptide data, all available HLA-DPA and DPB alleles were classified into one DP supertype. The available supertypes and corresponding alleles can be found on the download page of HLAsupE. |
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Usage of HLAsupE
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Search for HLA suppertype specific epitopes or peptidese
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“peptide sequence”: amino acid sequence coding with uppercase letters. example : "FLPSDFFPSV"
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Map HLA supertype-specific epitopes or peptides on an input protein sequence
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Search for the HLA supertype-specific epitopes or binding peptides by protein sequence, the protein name could give an arbitrary name. The protein sequence should be a plain sequence. Such as: |
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Search for mutated analogues of an input peptide
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Search for the mutated analogues of an input peptide, amino acid sequence coding with uppercase letters. example : "FLPSDFFPSV". |
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Search for promiscuous peptides presented by HLA molecules across supertypes
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Search for promiscuous peptides to alleles across HLA supertypes by the supertyps or source species, |
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NOTES
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HLAsupE and HLAsupB
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The query tools provided in the home page of HLAsupE aim to search for supertype-specific epitopes (T-cell activities), whereas the query tools for supertype-specific binding peptides (MHC-binding data) are provided in HLAsupB.
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Epitopes with the restrictions of serological HLA molecules
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The peptides presented by serological proteins were difficult to integrate into the supertype-specific dataset with an exact allele restriction. These data were only maintained in the T-cell activity and HLA-peptide binding data blocks; as a result, these peptide data can be displayed when a user inspects the detailed activity of a specific peptide, but a direct query of these peptides is currently unavailable in HLAsupE |
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Frequency of alleles
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The distribution of HLA genes in the human population varies with ethnicity and region. The frequency of alleles in a specific population should be taken into account. At present, Allele Frequency Net Database (AFND) and Population Coverage tool have been built to address this issue. |
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Update
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We will continue to update our database by extracting and curating HLA-restricted peptide data from all available epitope databases and published literature. We also encourage researchers to submit their own data to our database via email to wangshufeng81@hotmail.com. |
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2018-2023©copyright Institute of Immunology, Army Medical University and Bioinformatics Center of Chongqing |
contact: wangshufeng81@hotmail.com |