Protein haplotype sequences obtained by ProHap from the Haplotype Reference Consortium Release 1.1 dataset

<p>Database of protein sequences obtained using ProHap (<a href="https://github.com/ProGenNo/ProHap">https://github.com/ProGenNo/ProHap</a>) on the data set of phased genotypes published by the Haplotype Reference Consortium, Release 1.1 (<a href="https://ega-archive.org/datasets/EGAD00001002729" target="_blank" rel="noopener">https://ega-archive.org/datasets/EGAD00001002729</a>). We used Ensembl v.110 for the mapping of coordinates between genes, exons, and transcripts.</p> <p>Release 1.1 of the HRC is provided aligned with the GRCh37 reference genome. We have performed a liftover to the GRCh38 reference using GeneBe (https://genebe.net/tools/liftover). Variants for which the reported alternative allele is considered as reference in GRCh38 were removed. A threshold of 1% minor allele frequency was applied to filter the remaining variants. After translation, a frequency threshold of 0.5% was applied to filter the resulting unique non-canonical sequences. The complete configuration file for the ProHap run is attached to this repository.</p> <p>This dataset contains one compressed directory, contains the following files:</p> <ul> <li>F1: The concatenated fasta file ready to be used with search engines, contains the following: <ul> <li>Protein haplotype sequences obtained by ProHap</li> <li>Reference proteome as per Ensembl v. 110</li> <li>Contaminant sequences from the cRAP project (<a href="https://www.thegpm.org/crap/">https://www.thegpm.org/crap/</a>)</li> <li>The file is provided in two formats - full and simplified. The simplified fasta contains only the artificial protein identifier and the matching gene name, and is optimised for compatibility with a wide range of tools. For annotation of peptides using the PeptideAnnotator, please provide the header (F1.2) in addition to the fasta file.&nbsp;</li> </ul> </li> <li>F2: Additional information about the haplotype sequences, to be used for mapping identified peptides to the original haplotypes</li> <li>F3: Translations of haplotype cDNA sequences, before merging with the reference proteome</li> </ul> <p>For further description of the files, please refer to&nbsp;<a href="https://github.com/ProGenNo/ProHap/wiki/Output-files">https://github.com/ProGenNo/ProHap/wiki/Output-files</a>.</p> <p>For the usage of these databases with search engines, and downstream anaylsis of identified peptides, please refer to the project's wiki page: <a href="https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches">https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches</a>.</p> <p>When using these databases in your publication, please cite: Va&scaron;&iacute;ček, J., Kuznetsova, K.G., Skiadopoulou, D. <em>et al.</em> ProHap enables human proteomic database generation accounting for population diversity. <em>Nat Methods</em> (2024). <a href="https://doi.org/10.1038/s41592-024-02506-0">https://doi.org/10.1038/s41592-024-02506-0</a></p>