Julia (https://julialang.org) code to match pentatricopeptide repeat (PPR) protein sequences to likely RNA targets.
The software requires the ArgParse.jl and Statistics.jl packages to be installed.
The software uses scoring table to relate the the 5th/last amino acids of each PPR motif with the aligned nucleotide.
The original idea is from Barkan et al. Plos Genetics 8:e1002910. Several scoring tables are available to choose from.
Yan.tsv uses data from Yan et al. Nucleic Acids Res. 47:3728-3738; this is experimental data on binding of synthetic P-type PPR proteins to oligonucleotides in vitro.
Kobayashi.tsv uses data from Plant Cell Physiol. 60:862-874; this is from observed frequencies of different 5th/last combinations in alignments of natural PLS-type proteins to their target RNAs.
The Millman .tsv files are similarly derived from observed frequencies of different 5th/last combinations in alignments of natural PLS-type proteins to their target RNAs, but separate scoring tables have been derived for each type of PPR motif.
To run the software, install julia (instructions here: https://julialang.org/downloads/) and the ArgParse and Statistics packages (instructions here: https://datatofish.com/install-package-julia/)
PPRmatcher.jl requires three arguments:
- One or more PPR sequences in the output format from PPRfinder (https://github.com/ian-small/PPRfinder)
- One or more target seqeunces in fasta (or multifasta) format
- One or more scoring tables from the scoring_table directory
usage: PPRmatcher.jl [-r REFERENCE] [-e EDIT_SITE] [-s STRAND] [-o OUTFILE] [-h] PPR(s) target(s) scoring_table(s)...
positional arguments: PPR(s) path to file of PPRfinder motifs to search with target(s) path to file of FASTA format target sequence(s) to search in scoring_table(s) path to scoring table or directory of scoring table files
optional arguments: -r, --reference REFERENCE path to reference sequence for calculating score distribution -e, --edit_site EDIT_SITE edit site position within the sequence(s) (type: Int64, default: 0) -s, --strand STRAND which target strand(s) to match to (default: "F") -o, --outfile OUTFILE path to outfile for saving results -h, --help show this help message and exit
Examples of use cases:
#1 finding the probable target of mRPF2 in the nad6 transcript (the command below assumes that the pwd is PPRmatcher/test)
julia ../src/PPRmatcher.jl mRPF2.motifs.txt nad6.fasta ../scoring_tables/Yan.tsv
#2 finding the best matching editing site for the synthetic PPR dsn3PLS (the command below assumes that the pwd is PPRmatcher/test)
julia ../src/PPRmatcher.jl -e 41 dsn3PLS.motifs.txt cp_editing_sites.fasta ../scoring_tables/Kobayashi.tsv