Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and…

By Doug Hyatt, Gwo-Liang Chen, P. LoCascio, M. Land, F. Larimer, Loren J. Hauser

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Citations in the corpus

Clustering huge protein sequence sets in linear time (2017, methodology): “We predicted genes and protein sequences using Prodigal [19] resulting in 1,595,926,152 proteins.”
MGnify: the microbiome analysis resource in 2020 (2019, positive): “Approximately 25% of these sequences are predicted to be full length according to Prodigal’s gene identification criteria, with 15% truncated at either the N or C terminus and 60% predicted to be truncated at both ends (termed ‘partials’).”
DRAM for distilling microbial metabolism to automate the curation of microbiome function (2020, methodology): “Specifically, Prokka (30), MetaErg (32), and DRAM use Prodigal to call genes, while DFAST (31) uses MetaGeneAnnotator (55).”
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, methodology): “In conclusion, we have developed the new command-line software tool Bakta, and we demonstrated that it improves on existing rapid annotation tools for bacterial genomes in various ways: (i) Bakta outperforms existing tools in terms of functional annotation of CDSs over a broad taxonomic range of bot”
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (2017, methodology): “Protein sequences were predicted for each contig using Prodigal [81, 82] with the “meta” procedure (−p meta).”
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation (2018, background): “Protein sequences are predicted by calling Prodigal (21) if the query is genomes, or FragGeneScan (22) if the query is short DNAs from metagenomes or mRNAs or coding sequences of proteins.”
mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements (2021, methodology): “This setting was chosen because the alternative, -p single, requires 20,000 bp of training data which would not be possible for many of the MGEs (49).”
IMG/M 4 version of the integrated metagenome comparative analysis system (2013, methodology): “Protein-coding genes are identiﬁed using four ab initio gene calling tools: GeneMark (8), Metagene (9), Prodigal (10) and FragGeneScan (11).”
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) (2015, unknown): “2 ab initio gene prediction program [10].”