#PRF Search

This repository contains scripts that can be used to search through DNA sequences for the features that stimulate -1 programmed ribosomal frameshifting (PRF).

This pipeline was run on every annotated ORF in E. coli. If there was an intergenic region between one ORF and the next ORF, we added that region onto the 3' end of the first ORF.

Some large data files were not included in this repo due to their large size. The gammaproteobacteria database was found on NCBI refseq

#Dependencies

Rscape HMMER ViennaRNA

Python3:

argparse pandas json Bio.Seq re numpy math RNA (ViennaRNA Python wrapper) matplotlib shutil mlines datetime random

#Run commands

To run the whole pipeline:

bash search.sh -o E_coli_3p_utr -q mrna_plus_3utr.fa -d bacteria.1236.1.genomic.fna -r /path/to/your/installation/of/rscape_v1.6.1/bin/R-scape -p /path/to/this/repo/prf_search

To score sequences without running HMMER or CaCoFold:

python3 random_probability_eval.py -I All-genes-of-E.-coli-K-12-substr.-MG1655.fasta

To run pipeline on 4000 randomly generated sequences following E. coli gene length distribution:

python3 random_probability_eval.py -N 4000 -F All-genes-of-E.-coli-K-12-substr.-MG1655.fasta

To build a database from NCBI refseq

`python3 -I assembly_summary.txt -O bacteria_db.fa