This week I developed two programs to facilitate the development of my final program. The first program makes synonymous changes to a sequence extracted from a FASTA file. It does so by creating an array of codons in the sequence and modifying each codon with a synonymous one.
The second program takes an Rfold file as input and creates an array of nucleotide positions that are above a given threshold. It then creates three distinct arrays dependent on whether the amino acid that has a base-pairing probability above the specified threshold is in the first, middle, or last position in the codon.
I plan to integrate these two programs as a means to fulfill my current research objective. However, I am going to make large sections of code into subroutines as well as develop more dynamic methods of creating synonymous changes instead of hardcoding each possible codon into if-else statements.
The second program takes an Rfold file as input and creates an array of nucleotide positions that are above a given threshold. It then creates three distinct arrays dependent on whether the amino acid that has a base-pairing probability above the specified threshold is in the first, middle, or last position in the codon.
I plan to integrate these two programs as a means to fulfill my current research objective. However, I am going to make large sections of code into subroutines as well as develop more dynamic methods of creating synonymous changes instead of hardcoding each possible codon into if-else statements.