+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 labeled +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 steps are described in the +makeDoc, +the build scripts are in the +kent source tree, +and the track configuration is in +trackDb/contrib/hprc2annot. +
+ ++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 +
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