This track shows gene annotations produced by the Comparative Annotation Toolkit (CAT) for this Human Pangenome Reference Consortium (HPRC) Release 2 assembly. Genes are the stretches of DNA that are copied into RNA and, for most of them, translated into protein. Because each pangenome assembly is a newly sequenced human genome, its genes are not known in advance; CAT infers them by carrying a well-studied reference annotation across a whole-genome alignment onto the new assembly, and by combining that projection with direct transcript evidence. The result is a consistent set of gene models for every assembly, which makes it possible to compare the same gene across many individuals.
Genes follow the standard UCSC gene display: boxes are exons, connecting lines are introns, and arrows on the introns show the direction of transcription. Thicker boxes mark the coding portion (CDS) and thinner boxes the untranslated regions (UTRs). Where the browser is zoomed in far enough, the amino-acid translation and, on request, the underlying bases are shown. Items are labelled by gene name where a name was available from the reference; the transcript identifier and the gene and transcript biotypes are shown on the item details page. Both gene name and transcript identifier are searchable.
The Comparative Annotation Toolkit projects an existing high-quality reference annotation onto a target genome through a whole-genome (Cactus/progressiveCactus) alignment, reconciles the projected transcripts with ab initio and transcript-based evidence, and produces a filtered consensus gene set with stable cross-assembly identifiers. See the reference below for the full algorithm. For the HPRC pangenome, CAT was run against the CHM13/GRCh38-based reference annotation to annotate each assembly.
The annotation files were obtained from the HPRC Release 2 data collection on the public s3://human-pangenomics bucket, indexed at the hprc_intermediate_assembly data tables. Each per-assembly GFF3 was converted to a UCSC bigGenePred file with gff3ToGenePred and genePredToBigGenePred; gene symbols and gene and transcript biotypes from the GFF3 were carried into the display fields. The build scripts are in the kent source tree.
For automated analysis, the annotation is stored in a bigBed-format file (catGenes.bb) that can be read with the UCSC tool bigBedToBed, which can be compiled from source or downloaded as a precompiled binary. It can also extract features for a region, for example: bigBedToBed catGenes.bb -chrom=CM085953.1 -start=0 -end=100000 stdout. The original annotation files are available from the HPRC S3 bucket linked above.
Annotations were generated by the Human Pangenome Reference Consortium. Thanks to the HPRC production team for making these data available.
Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE et al. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 Jul;28(7):1029-1038. PMID: 29884752; PMC: PMC6028123