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