The source code is available at the bottom of this answer or from this gist. Each thread would work on "rc"-ing sequences in its own piece of the array.Īnother python extension but without cython. If you have many thousands of sequences stored in memory, you could split an array of sequences up into smaller arrays by use of offsets or array indices. It's unclear how "pure" the answer needs to be, but making a system call from Python seems fair if you're processing strings and your goal is performance.Īnother direction to take may be to look at multithreading, if you don't need ordered output. Try our oligo calculator to determine volumes needed to resuspend your DNA oligos to desired concentrations, estimate the percentage of full-length product for different oligo lengths, and calculate final yield based on oligo length, synthesis scale, and purification method. Outsourcing the reverse complement step to a utility written in C will almost always beat the best that Python can do, and you can do nice and important things like bounds checking etc. You might be able to use this directly in Python via the subprocess library. or its reverse complement (whichever is lexicographically smaller). The reverse complement allows you to maintain 5’ to 3’ orientation. Here is my fast implementation of a reverse complement function in C: Circular uSEGUID or cSEGUID is the uSEGUID checksum for circular (DNA) sequences. Home Tools DNA Reverse Complement DNA Reverse Complement Type or paste your DNA sequence below and automatically retrieve the reverse, complement, or reverse complement sequence. This would replace the nest of if statements and probably give a nice little boost ( and it appears it does, making it among the best performers so far!). One easy way to speed this up is to use a static const unsigned char array as an ASCII lookup table, which maps a residue directly to its complement. #!/usr/bin/env pythonĬomplement = % increase over baseline""".format( Formula moles dsDNA (mol) mass of dsDNA (g)/ ( (length of dsDNA (bp) x 617.96 g/mol/bp) + 36. What is the fastest way to get the reverse complement of a sequence in python? I am posting my skeleton program to test different implementations below with DNA string size 17 as an example. The pairing of nucleotides within the DNA double-helix is complementary which. Line profiling programs indicate that my functions spend a lot of time getting the reverse complements, so I am looking to optimize. A DNA sequence whose 5-to-3 sequence is identical on each DNA strand. This program converts a nucleotide (DNA/RNA) sequence into complement, reverse, or reverse complement sequence. I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. The existing DNA based image cryptosystems, their DNA coding scheme just employs four DNA symbols, namely A, T, C and G, to represent the four binary two-tuples, namely 00b, 01b, 10b and 11b, respectively.
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