Schema for Poran HLA II - RECON HLA-II epitopes
  Database: wuhCor1    Primary Table: poranHla2 Data last updated: 2020-04-17
Big Bed File: /gbdb/wuhCor1/bbi/poranHla/CD8-hla2.bb
Item Count: 5,352
Format description: poran_hla2 bed9+2 track
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart19861Start position in chromosome
chromEnd19934End position in chromosome
nameANTVIWDYKRDAPAHISTIGVCSMTName or ID of item, ideally both human readable and unique
score0Score (0-1000)
strand++ or - for strand
thickStart19861Start of where display should be thick (start codon)
thickEnd19934End of where display should be thick (stop codon)
reserved58,76,192RGB value (use R,G,B string in input file)
id2134ID of peptide
name2orf1ab_polyprotein_ANTVIWDYKRDAPAHISTIGVCSMT_DRB3_0301;DRB3_0101;DQB1-0202_DQA1-0201Protein name and restrictions to HLA-II

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedidname2
NC_045512v21986119934ANTVIWDYKRDAPAHISTIGVCSMT0+198611993458,76,1922134orf1ab_polyprotein_ANTVIWDYKRDAPAHISTIGVCSMT_DRB3_0301;DRB3_0101;DQB1-0202_DQA1-0201
NC_045512v21986419937NTVIWDYKRDAPAHISTIGVCSMTD0+198641993758,76,1922135orf1ab_polyprotein_NTVIWDYKRDAPAHISTIGVCSMTD_DRB3_0301;DRB3_0101;DQB1-0202_DQA1-0201
NC_045512v21986719940TVIWDYKRDAPAHISTIGVCSMTDI0+198671994058,76,1922136orf1ab_polyprotein_TVIWDYKRDAPAHISTIGVCSMTDI_DRB3_0301;DRB3_0101;DQB1-0202_DQA1-0201
NC_045512v21987019943VIWDYKRDAPAHISTIGVCSMTDIA0+198701994358,76,1922133orf1ab_polyprotein_VIWDYKRDAPAHISTIGVCSMTDIA_DRB3_0301;DRB3_0101;DQB1-0202_DQA1-0201
NC_045512v21987319946IWDYKRDAPAHISTIGVCSMTDIAK50+1987319946111,145,2421702orf1ab_polyprotein_IWDYKRDAPAHISTIGVCSMTDIAK_DQB1-0502_DQA1-0102;DRB3_0101;DRB3_0301;DQB1-0202_DQA1-0201
NC_045512v21987619949WDYKRDAPAHISTIGVCSMTDIAKK84+1987619949151,184,2541524orf1ab_polyprotein_WDYKRDAPAHISTIGVCSMTDIAKK_DQB1-0502_DQA1-0102;DRB3_0101;DQB1-0202_DQA1-0201;DRB3_0301;DQB1-0201_DQA1-0201
NC_045512v21987919952DYKRDAPAHISTIGVCSMTDIAKKP84+1987919952149,183,2543363orf1ab_polyprotein_DYKRDAPAHISTIGVCSMTDIAKKP_DQB1-0502_DQA1-0102;DQB1-0201_DQA1-0201;DPB1-1101_DPA1-0201;DQB1-0202_DQA1-0201
NC_045512v21988219955YKRDAPAHISTIGVCSMTDIAKKPT84+1988219955149,183,2543364orf1ab_polyprotein_YKRDAPAHISTIGVCSMTDIAKKPT_DQB1-0502_DQA1-0102;DQB1-0201_DQA1-0201;DPB1-1101_DPA1-0201;DQB1-0202_DQA1-0201
NC_045512v21988519958KRDAPAHISTIGVCSMTDIAKKPTE103+1988519958172,200,2521901orf1ab_polyprotein_KRDAPAHISTIGVCSMTDIAKKPTE_DQB1-0502_DQA1-0102;DQB1-0501_DQA1-0101;DQB1-0202_DQA1-0201;DQB1-0201_DQA1-0201;DPB ...
NC_045512v21988819961RDAPAHISTIGVCSMTDIAKKPTET103+1988819961172,200,2521899orf1ab_polyprotein_RDAPAHISTIGVCSMTDIAKKPTET_DQB1-0502_DQA1-0102;DQB1-0501_DQA1-0101;DQB1-0202_DQA1-0201;DQB1-0201_DQA1-0201;DPB ...

Poran HLA II (poranHla2) Track Description
 

Description

This track shows putative epitopes for CD4+ and CD8+ T cells whose HLA binding properties cover over 99% for US, European, and Asian populations, for both HLA-I and HLA-II. The track includes 11,776 CD8 epitopes restricted to HLA-I as predicted by RECON. All the epitopes are scored using a combined coverage score reported for USA, EUR, and API. Specifically, score = (USA_coverage+EUR_coverage+API_coverage)*1000/3.

For more details, see here.

Display Conventions and Configuration

Genomic locations of epitopes are labeled with a unique ID. Mousing over an item shows the protein name and restrictions to HLA-I. A click on an item shows a standard feature detail page with the both the ID and the mouse over information.

Methods

For a full description of the methods used, refer here.

Data Access

The raw data can be explored interactively with the Table Browser, or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/poranHla/CD8-hla1.bb -chrom=NC_045512v2 -start=0 -end=29902 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

References

Asaf Poran, Dewi Harjanto, Matthew Malloy, Michael S. Rooney, Lakshmi Srinivasan, Richard B. Gaynor. Sequence-based prediction of vaccine targets for inducing T cell responses to SARS-CoV-2 utilizing the bioinformatics predictor RECON. bioRxiv 2020.04.06.027805