Marker panels and genetic codes¶
Every query is scored against a fixed set of HMM marker panels. Each panel contributes a completeness column and, where applicable, a duplication column to the summary table. Gene calling for nucleotide input is run under nine genetic codes, and the selected code is recorded per query.
Marker panels¶
| Panel | Column prefix | Size | Purpose |
|---|---|---|---|
| GVOG4 | gvog4 |
n/4 | Core NCLDV single-copy orthologs |
| GVOG8 | gvog8 |
n/8 | Core NCLDV single-copy orthologs |
| BUSCO eukaryotic | busco |
n/255 | Eukaryotic carry-over flag |
| Universal COG (UNI56) | cog |
n/56 | Universal cellular carry-over flag |
| Mryavirus | mrya |
n/6 | Mryavirus markers |
| Phage (geNomad) | phage |
n/20 | Phage contamination flag |
| Virophage core | vp |
n/4 | MCP, Penton, ATPase, Protease |
| Mirusviricota core | mirus |
n/4 | MCP, ATPase, Portal, Triplex |
| Capsid typing | capsid_group, ncldv_mcp_total |
count | Capsid (MCP) type tally |
| PPV flag | plv |
count | A32 (PLV_PC_054) proteins placing with PPV references |
For each panel, {panel}_completeness reports distinct marker models present over panel size (for example 8/8), and {panel}_dup reports total hits over distinct models present (a duplication factor).
Note
Two panels deviate from the {panel}_dup convention. The virophage panel emits vp_completeness and vp_mcp (count of VP MCP hits), not vp_dup. The Mirusviricota panel emits mirus_completeness only. capsid_group is a label:count tally across the Nucleocytoviricota and Mirusviricota phyla and the Bellas & Sommaruga capsid groups; ncldv_mcp_total is the NCLDV-specific MCP count; plv counts A32 proteins (PLV_PC_054) that place with PPV references and flags Polinton-like viruses and virophages within the PPV (Preplasmiviricota) domain. It is 0 for ordinary NCLDV.
Each marker model carries a majority functional annotation derived from its member proteins. The full per-model table is in Marker annotations.
Order-level markers are a separate panel of 576 order-conserved orthologous groups, built only when fast mode is off (-e/--extended). The default fast mode skips them. See Tune speed and accuracy for the speed and resolution trade-off.
Per-column definitions for the full summary table are in Output reference; interpretation of completeness, contamination, and duplication is in Quality metrics.
Genetic codes¶
Nine genetic codes are tested during gene calling:
| Code | Translation table |
|---|---|
| 0 | Pyrodigal meta mode (pretrained models) |
| 1 | NCBI standard |
| 4 | NCBI mold, protozoan, coelenterate mitochondrial; Mycoplasma, Spiroplasma |
| 6 | NCBI ciliate, dasycladacean, hexamita nuclear |
| 11 | NCBI bacterial, archaeal, plant plastid |
| 15 | NCBI Blepharisma nuclear |
| 29 | NCBI Mesodinium nuclear |
| 106 | Genetic code similar to code 6, found in some novel giant virus genomes |
| 129 | Genetic code similar to code 29, found in some novel giant virus genomes |
Every code above is tested for every nucleotide query. This is not configurable; see Configuration reference.
Selection rule, applied per query:
- Start from meta (code 0).
- Replace it when another code yields at least 2 more complete marker hits.
- Or an average best-hit score at least 10 percent higher.
- Or a coding density at least 5 percent higher.
Any one of the three conditions is sufficient.
The selected code is written to the ttable column. When the pyrodigal meta model wins, ttable reads codemeta. Protein (.faa) input skips gene calling and reports ttable no_fna, and its nucleotide statistics (GCperc, CODINGperc) are 0.00.
For the full gene-calling and marker-detection sequence, see How it works.