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My Submission for the Applied F# Challenge
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README.md

Primer design for qPCR with F# and bioContainers - my submission for the applied F# challenge

Kevin Schneider

This submission focuses on the power of F# regarding quick establishment of bioinformatic workflows. In fact, the code in this repository was written in about 3 days. We use F# in our (computer)lab @CSBiology for all kinds of data analysis (scripting) and software development.

This Library is the result of a refactored script I developed for qPCR primer design. It uses 4 parameters to access if the primers are usable:

  • interaction free energy of the fwd and rev primer with each other
  • interaction free energy of the primer with itself
  • interaction free energy of intramolecular loop formation
  • the "badness" of the best blast result of the primer against the cDNA library that is not a match with the sequence itself

I leveraged BioFSharp.BioTools to make two bioinformatic tools usable in F# from docker container to calculate these features:

  • IntaRNA - a tool for predicting interactions between nuctleotides (this includes various hybridization energy calculations)
  • BlastN - The classic Basic Local Alignment Search Tool

For exploratory data analysis, i used Deedle.

The output is a frame containing the features for fwd and rev primer sets:

ExampleResult

Prerequisites

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