prfect 0.34

A tool to predict programmed ribosomal frameshifts

prfect

PRFect is a tool to predict programmed ribosomal frameshifting in eukaryotic, prokaryotic, and viral genomes

The manuscript is currently in review and has been preprinted on bioRxiv:

https://www.biorxiv.org/content/10.1101/2023.04.10.536325v1

It takes as input the genome and its annotated CoDing Sequence (CDS) as a GenBank file. It searches through the file looking for 8 different slippery site motifs associated with backwards (-1) frameshifts and two motifs associated with forward (+1) frameshifts. When a motif is encountered, various cellular properties and contributing factors are assessed and a prediction is made whether the site is indeed involved in programmed ribosomal frameshifting.

To install:

pip3 install prfect

To run:

prfect.py input.gbk

An example genome for SARS-Cov2 is provided in the test folder. The SARS-Cov2 genome contains 12 genes the first of which happens to be a PRF gene and is denoted as such through the use of the join keyword. Any genes already present that use the join keyword are split into their two parts and subsequently predicted anew and then tagged with the /label=1 feature tag to indicate a TruePositive. When the genome is run through PRFect the known PRF gene is correctly predicted to utilize programmed ribosomal frameshifting.

$ prfect.py test/covid19.gbk 

     CDS             join(266..13468,13468..21555)
                     /ribosomal_slippage
                     /direction=-1
                     /motif=is_threethree
                     /slippery_sequence=tttaaac
                     /label=1
                     /locus=NC_045512
                     /product="ORF1ab polyprotein"
                     /product="ORF1ab polyprotein"

Another example is bacteriophage lambda, which has the geneG and geneGT tail assembly chaperone gene that is known to frameshift. The current genbank annotation file (NC_001416) does not have the gene properly denoted with the join keyword and so both pieces are in two separate CDS features. When the genome is run through PRFect the gene is correctly identified as being a single PRF gene with the /label=0 to indicate that it is an UnknownPositive.

$ prfect.py test/lambda.gbk

     CDS             join(9711..10115,10115..10549)
                     /ribosomal_slippage
                     /direction=-1
                     /motif=is_threethree
                     /bases=gggaaag
                     /label=0
                     /locus=NC_001416
                     /product="minor tail protein G"
                     /product="tail assembly protein T"