The PGAP pipeline is designed to annotate both complete genomes and draft genomes comprising multiple contigs. PGAP is deeply integrated into NCBI infrastructure and processes, and uses a modular software framework, GPipe, developed at NCBI for execution of all annotation tasks, from fetching of raw and curated data from public repositories (the Sequence and Assembly databases) through sequence alignment and model-based gene prediction, to submission of annotated genomic data to public NCBI databases.
On input, PGAP accepts an assembly (either draft or complete) with a predefined NCBI Taxonomy ID that defines the genetic code of the organism. PGAP also accepts a predetermined clade identifier, matching the genome in question to a species-specific clade. Clade IDs are computed using a series of 23 universal ribosomal protein markers and are independent of taxonomy. In the absence of a clade ID, we can infer the ID from taxonomy in the majority of cases. The clade ID determines the realm of core proteins used as the target protein set. PGAP annotation of a new genomic sequence can be requested at the time of submission to GenBank. Taxonomic and clade identifiers are determined outside of the annotation pipeline, and are influenced by GenBank curatorial decisions. The clade-dependent sets of protein clusters as well as sets of curated structural ribosomal RNAs (5S, 16S and 23S) are generated and maintained outside of PGAP. More details on the PGAP workflow are provided below.
On input, PGAP accepts an assembly (either draft or complete) with a predefined NCBI Taxonomy ID that defines the genetic code of the organism. PGAP also accepts a predetermined clade identifier, matching the genome in question to a species-specific clade. Clade IDs are computed using a series of 23 universal ribosomal protein markers and are independent of taxonomy. In the absence of a clade ID, we can infer the ID from taxonomy in the majority of cases. The clade ID determines the realm of core proteins used as the target protein set. PGAP annotation of a new genomic sequence can be requested at the time of submission to GenBank. Taxonomic and clade identifiers are determined outside of the annotation pipeline, and are influenced by GenBank curatorial decisions. The clade-dependent sets of protein clusters as well as sets of curated structural ribosomal RNAs (5S, 16S and 23S) are generated and maintained outside of PGAP. More details on the PGAP workflow are provided below.
