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### Prodigal ORF Prediction (`prodigal-prediction`) Predicts protein-coding genes in one or more prokaryotic DNA sequences using Prodigal through the pyrodigal interface. Each returned gene carries its nucleotide and translated amino-acid sequence, 1-indexed start and end coordinates on the parent sequence, strand, reading frame, partial-gene status, [GC content](https://en.wikipedia.org/wiki/GC-content), start codon identity, and the detected ribosome binding site motif and spacer. #### API Reference

Source DNA sequence(s) to analyze for genes and open reading frames. Can be provided as:

Source Use meta mode for gene prediction. Options: NCBI genetic code for translation. Only used in single-genome mode (`meta_mode=False`). In meta mode, pre-trained metagenomic models use their own built-in translation tables and this parameter is ignored. Common options: Available options: `standard`, `vertebrate_mitochondrial`, `yeast_mitochondrial`, `mycoplasma`, `invertebrate_mitochondrial`, `ciliate_nuclear`, `echinoderm_mitochondrial`, `euplotid_nuclear`, `bacterial`, `alternative_yeast_nuclear`, `ascidian_mitochondrial`, `alternative_flatworm_mitochondrial`, `blepharisma_nuclear`, `chlorophycean_mitochondrial`, `trematode_mitochondrial`, `scenedesmus_mitochondrial`, `thraustochytrium_mitochondrial`, `rhabdopleuridae_mitochondrial`, `candidate_division_sr1` Prevent genes from running off sequence edges. Options: When `True`, treat runs of N bases as masked and do not call genes spanning them (equivalent to prodigal's `-m`). Default: `False`. Minimum gene length in nucleotides. Default: 90. Drop for draft assemblies where short fragments are expected. Number of CPU threads for parallel processing of multiple sequences. Higher values speed up batch processing. By default, automatically detects and uses all available CPU cores. Must be at least 1. Default: auto-detect all cores. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source One entry per input sequence, in input order, each holding the ORFs found in that sequence. ORFs found in this sequence, in the caller's order.

#### Applications This tool is appropriate for the gene-calling step of any analysis that begins with raw prokaryotic DNA sequences and needs a curated set of protein-coding genes rather than an exhaustive enumeration of all open reading frames. Representative applications include initial gene annotation of a newly assembled bacterial or archaeal genome, recovery of protein-coding genes from metagenomic contigs for downstream functional or taxonomic analysis, and generation of translated protein sequences for subsequent homology search or domain annotation. #### Usage Tips * **`meta_mode` selects the operating mode and is the most consequential setting.** The default of `meta_mode=True` applies a panel of pre-trained parameters that is appropriate for short contigs, draft assemblies, and metagenomic samples. A value of `meta_mode=False` instead trains scoring parameters on the input sequence itself and requires at least approximately 100 kilobases of input for reliable training. The single-genome mode is appropriate for complete or near-complete genomes when sufficient training sequence is available. * **`translation_table` selects the [genetic code](https://en.wikipedia.org/wiki/Genetic_code) and is only consulted in single-genome mode.** In meta mode the pre-trained metagenomic models carry their own internal translation tables, and this parameter has no effect on the output. The default value of `"bacterial"` corresponds to NCBI table 11 (bacterial, archaeal, and plant plastid code). A value of `"mycoplasma"` selects NCBI table 4 (Mycoplasma and Spiroplasma), and `"standard"` selects NCBI table 1 (the standard genetic code). Additional supported NCBI tables are appropriate for organisms that use the corresponding alternative codes. * **`closed_ends` controls whether partial genes at sequence boundaries are reported.** The default of `closed_ends=False` allows partial genes at the 5' and 3' ends of each input sequence, which is appropriate for linear contigs and draft assemblies in which real genes may extend across the assembly boundary. A value of `closed_ends=True` prevents partial-gene predictions and is appropriate for complete circular genomes such as bacterial chromosomes and plasmids, in which there are no true sequence ends. * **`min_gene` is the minimum gene length in nucleotides and defaults to 90.** This corresponds to approximately 30 amino acids. Lower values can be considered for draft assemblies in which short gene fragments are expected at contig boundaries, while higher values are appropriate when only larger, well-defined genes are of interest. * **`mask=True` excludes regions of unresolved nucleotides from gene calling.** When the input contains runs of `N` characters representing low-quality or gap regions, a value of `mask=True` prevents Prodigal from calling genes that span those regions, which is appropriate for draft assemblies with significant unresolved sequence content. * **Partial-gene status is reported as a two-digit code on each predicted gene.** A status of `00_00` indicates a complete gene with both a start and a stop codon present in the input. A status of `10_00` indicates a gene that is truncated at the 5' end of the input, `00_01` indicates truncation at the 3' end, and `10_01` indicates truncation at both ends. Partial genes commonly represent real coding sequences that extend beyond the boundary of the input and should not be excluded from downstream analyses without consideration.