Publications

Citation

When citing Pyrodigal, please additionally cite the original Prodigal paper, which developed the actual method. You can for instance cite both papers as: Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyatt et al., 2010).

Use the following for the bibliography:

• Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). doi:10.1186/1471-2105-11-119.

• Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296. doi:10.21105/joss.04296.

Or just grab the BibTex file with these two papers.

JOSS

Pyrodigal has been published in the Journal of Open-Source Science. JOSS is a community-run journal and relies upon volunteer effort. If you’d like to support JOSS please consider doing either one (or both) of the the following:

• Volunteering to review for JOSS sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html.

• Making a small donation to support running costs here: https://numfocus.org/donate-to-joss.

Users

Pyrodigal is being used in the following research works:

• Carroll, L. M., Larralde, M., Fleck, J. S., Ponnudurai, R., Milanese, A., Cappio, E., Zeller, G. Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv 2021.05.03.442509; doi:10.1101/2021.05.03.442509.

• Santos-Júnior C.D., Pan, S., Zhao, X., Coelho, L.P. Macrel: antimicrobial peptide screening in genomes and metagenomes. PeerJ 8:e10555. doi:10.7717/peerj.10555.

• Sirén K., Millard, A., Petersen, B., Gilbert, M. T. P., Clokie, M. RJ., Sicheritz-Pontén, T. Rapid discovery of novel prophages using biological feature engineering and machine learning. bioRxiv 2020.08.09.243022; doi:10.1101/2020.08.09.243022.

• Turkington, C. J. R., Nezam Abadi, N., Edwards, R. A., Grasis, J. A. hafeZ: Active prophage identification through read mapping. bioRxiv 2021.07.21.453177; doi:10.1101/2021.07.21.453177.

• Reynolds, R., Hyun, S., Tully, B., Bien, J., Levine, N. M. Identification of microbial metabolic functional guilds from large genomic datasets. Front Microbiol. 2023 Jun 30;14:1197329. doi:10.3389/fmicb.2023.1197329..

Feel free to get in touch to add yours to the list!