Flowchart.txt

Pseudo-code for Tavtigian BRCA1 RNG domain mutation screen
Brett Milash
02/07/2017

Given the wild-type BRCA1 RNG domain DNA sequence, the coordinates of the 
region that will be synthesized, and the sub-region that will be mutated:

	1. Generate the wild-type protein sequence encoded by the mutated 
		region.

	2. Generate all mis-sense substitutions to the WT protein sequence that 
		are possible from single nucleotide substitutions to the WT
		nucleotide sequence, and the corresponding DNA sequence that
		encodes that mis-sense substitution.

	3. Generate protein sequences that comprise an alanine scan, ie the 
		protein sequences that arise from an insertion of a single
		alanine amino acid at each position in the WT protein sequence,
		and the corresponding DNA sequences that code for each 
		protein sequence.
	
	4. For each DNA / protein sequence pair generated in steps 2 and 3:

		4a. Generate 5 to 8 variations on this sequence by adjusting 
			the wobble bases in codons to alter the nucleotide
			sequences without altering the protein sequence.

		4b. Apply the following tests to screen the nucleotide sequences
			from 4a, to exclude the following:

			- new splice donors / acceptors

			- GGGG sequences

			- poly-X of length 6 or greater for any nucleotide

			- sequences with GC content > 0.75 or below 0.25.

			- rare codon usage

			- stable secondary structures

			- exon exclusion signals

		4c. Report the sequences that pass the filters in 4b in a the
			proper format for ordering oligonucleotides.