prodigal
Microbial (bacterial and archaeal) gene finding program
Install
- All systems
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curl cmd.cat/prodigal.sh
- Debian
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apt-get install prodigal - Ubuntu
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apt-get install prodigal - Kali Linux
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apt-get install prodigal - Windows (WSL2)
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sudo apt-get updatesudo apt-get install prodigal - OS X
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brew install prodigal - Raspbian
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apt-get install prodigal - Dockerfile
- dockerfile.run/prodigal
prodigal
Microbial (bacterial and archaeal) gene finding program
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include: Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less. Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly). Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%. GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations. Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown. Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.