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I am having possibly a simple question which is proving difficult.

My objective is to take the reference FASTA file and flat file database with 1500 restriction enzymes with its cutting sites (mostly pattern I would say).

  1. I first want to see that how many times each enzyme cut the FASTA file and;
  2. second to check the number and size of fragment that each enzyme would give me, this output pregerably would be a CSV file may be.

Background I tried to do pattern search using R, but its just collapsing my system. I am looking for bash command may be.

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  • $\begingroup$ This looks like the RAM load of the reg-ex in R. Bash isn't the best for reg-ex style commands IMO, Python can do this, I would assume awk too, and dare I say Perl is really good. $\endgroup$
    – M__ ♦
    Commented Nov 1, 2022 at 14:34

2 Answers 2

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Biopython has a module dedicated to working with restriction enzymes. Without any code examples we cannot help you much further.

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The diffHic package might have solved this issue in R.

# Load the genomic data
genome <- biostrings::readDNAStringSet("your_file.fa")

# Run the in silico restriction digest 
cuts <- cutGenome(genome, "CCGCGG", overhang=2L) # SacII

the cuts GRanges object contains the boundaries of each restriction fragment for given genome.

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