Finalizing inputs

Schrick-Noah_CS-6643_Lab-9.R

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+# Lab 9 for the University of Tulsa's CS-6643 Bioinformatics Course
+# Pairwise Sequence Alignment with Dynamic Programming
+# Professor: Dr. McKinney, Fall 2022
+# Noah L. Schrick - 1492657
+
+## Set Working Directory to file directory - RStudio approach
+setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
+
+
+#### Part A: Specifying the Input
+## Score Rules and Seqs
+x_str <- "ATAC"   # side sequence
+y_str <- "GTGTAC" # top sequence
+match_score <- 3
+mismatch_score <- -1
+gap_penalty <- -4
+
+## Substitution Matrix
+dna.letters<-c("A","C","G","T")
+num.letters <- length(dna.letters)
+S<-data.frame(matrix(0,nrow=num.letters,ncol=num.letters))  # data frame
+rownames(S)<-dna.letters; colnames(S)<-dna.letters
+for (i in 1:4){
+  for (j in 1:4){
+    if(dna.letters[i]==dna.letters[j]){ 
+      S[i,j]<- match_score
+    }
+    else{ 
+      S[i,j]<- mismatch_score
+    }
+  }
+}
+