read.prodigal: Read a Prodigal gene finding output file
In cstubben/genomes2: Genome sequencing project metadata

Description Usage Arguments Details Value Author(s) References See Also Examples

Read a gff formatted Prodigal gene output file from NCBI (version 2.5)

1	read.prodigal(file, allScores = FALSE)

`file`	Prodigal gff output file
`allScores`	include all scores

Prodigal output files are available from the NCBI genomes ftp directory, ftp://ftp.ncbi.nih.gov/genomes.

GRanges with 7 elementMetadata columns: id, partial flag for genes continuing off the edge of a contig, start codon, RBS motif, RBS spacer, coding potential/score and start score.

If allScores is TRUE, then four additional score columns are included: total score (sum of coding and start score) and RBS motif score, upstream region score, and codon type score (which usually sum to start score). See the README file in the Prodigal distribution for complete details.

Chris Stubben

Prodigal is a microbial gene finding program developed at University of Tennessee and Oak Ridge National Laboratory. See http://prodigal.ornl.gov for details

read.ncbi.ftp

 file<-"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Yersinia_pestis_CO92_uid57621/NC_003143.Prodigal-2.50" 
 x <-read.prodigal(file)
 x
 metadata(x)
 table2(values(x)$start_type)
 table2(values(x)$rbs_motif)
 hist(values(x)$sscore, br=40, col="blue", main="", xlab="Start score")