run.prodigal: Finding coding genes
| run.prodigal | R Documentation |
Finding coding genes
Description
Finding coding genes in genomic DNA using the Prodigal software.
Usage
run.prodigal(
genome_file = system.file("extdata/examples/2619619645/in", "2619619645.genes.fna",
package = "microtrait", mustWork = TRUE),
fa_file = gsub(".fna", ".prodigal.fa", genome_file),
faa_file = gsub(".fna", ".prodigal.faa", genome_file),
mode = "single",
transtab = 11,
maskN = FALSE,
bypassSD = FALSE
)
Arguments
genome.file |
A FASTA file with the genome sequence(s). |
faa.file |
If provided, prodigal will output all proteins to this fasta-file (text). |
proc |
Either |
mask.N |
Turn on masking of N's (logical) |
bypass.SD |
Bypass Shine-Dalgarno filter (logical) |
Details
The external software Prodigal is used to scan through a prokaryotic genome to detect the protein coding genes. This free software can be installed from https://github.com/hyattpd/Prodigal.
In addition to the standard output from this function, FASTA files with protein and/or DNA sequences may
be produced directly by providing filenames in faa.file and ffn.file.
The input proc allows you to specify if the input data should be treated as a single genome
(default) or as a metagenome.
The translation table is by default 11 (the standard code), but table 4 should be used for Mycoplasma etc.
The mask.N will prevent genes having runs of N inside. The bypass.SD turn off the search
for a Shine-Dalgarno motif.
Value
prodigal outputs
Note
The prodigal software must be installed on the system for this function to work, i.e. the command ‘system("prodigal -h")’ must be recognized as a valid command if you run it in the Console window.
