predict‐genes‐prodigal

This action uses Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm), a gene prediction method designed for improved gene structure prediction, translation initiation site recognition, and reduced false positives in prokaryotic genomes.

For the full description of the action's inputs, outputs, and parameters run qiime moshpit evaluate-busco --help in the terminal.

Inputs

• mags (FeatureData[MAG]): MAGs to be analyzed.

Outputs

• loci (GenomeData[Loci]): Gene coordinates files (one per MAG) listing the location of each predicted gene as well as some additional scoring information.
• genes (GenomeData[Genes]): Fasta files (one per MAG) with the nucleotide sequences of the predicted genes.
• proteins (GenomeData[Proteins]): Fasta files (one per MAG) with the protein translation of the predicted genes.

Citation

@article{key0,
 author = {Hyatt, Doug and Chen, Gwo-Liang and LoCascio, Philip F. and Land, Miriam L. and Larimer, Frank W. and Hauser, Loren J.},
 doi = {10.1186/1471-2105-11-119},
 issn = {1471-2105},
 journal = {BMC Bioinformatics},
 keywords = {Bias Score, Codon Position, Halobacterium Salinarum, Ribosomal Binding Site, Translation Initiation Site},
 month = {March},
 number = {1},
 pages = {119},
 shorttitle = {Prodigal},
 title = {Prodigal: prokaryotic gene recognition and translation initiation site identification},
 url = {https://doi.org/10.1186/1471-2105-11-119},
 urldate = {2023-10-23},
 volume = {11},
 year = {2010}
}