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