Calculating tetranucleotide (k-mer) frequencies

• perl-for-reysenbach-lab

  3 3 10.0 Perl

  These are perl scripts I developed over many years as a Bioinformaticist for the Reysenbach Lab at PSU. The Reysenbach Lab studies microbial diversity in extreme environments. Lotta fasta utilities here if you are into that sort of thing.

In 2016 I wrote a Perl script for the Reysenbach lab that calculates k-mer frequencies, for all k-mers in a given sequence. It was made public soon after, and you can find get_kmer_frequencies.pl on my Github page.

• python-bioinformatics

  1 0 0.0 Python

  Here are five of my bioinformatics scripts that have been converted from Perl to Python... Also a script for creating histograms of GC content.

This script is available for download on my GitHub page. To test for speed, I ran these two scripts five times each with two different sequence examples; a full genome file containing one long fasta record, and a Metagenome Assembled Genome (MAG) file containing 1708 shorter fasta records. Python was 2.9 times faster than Perl for the full genome, and 2.1 times faster than Perl for the MAG. I’ve recently become aware of the optimizing compiler RPerl, which allows Perl to be compiled into “ultra-fast and fully-compatible” C++, so I’m excited to try this out and see how the results compare to both Perl and Python.

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