dna_rna

DNA dizisi tanımlama

dna_sequence <- "ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG"

DNA -> RNA transkripsiyonu

transcribe_dna_to_rna <- function(dna) {
  dna <- toupper(dna)
  rna <- chartr("T", "U", dna)
  return(rna)
}

rna_sequence <- transcribe_dna_to_rna(dna_sequence)
cat("RNA Sequence: ", rna_sequence, "\n")

## RNA Sequence:  AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG

Kodon tablosu

codon_table <- c(
  UUU = "F", UCU = "S", UAU = "Y", UGU = "C",
  UUC = "F", UCC = "S", UAC = "Y", UGC = "C",
  UUA = "L", UCA = "S", UAA = "Stop", UGA = "Stop",
  UUG = "L", UCG = "S", UAG = "Stop", UGG = "W",
  CUU = "L", CCU = "P", CAU = "H", CGU = "R",
  CUC = "L", CCC = "P", CAC = "H", CGC = "R",
  CUA = "L", CCA = "P", CAA = "Q", CGA = "R",
  CUG = "L", CCG = "P", CAG = "Q", CGG = "R",
  AUU = "I", ACU = "T", AAU = "N", AGU = "S",
  AUC = "I", ACC = "T", AAC = "N", AGC = "S",
  AUA = "I", ACA = "T", AAA = "K", AGA = "R",
  AUG = "M", ACG = "T", AAG = "K", AGG = "R",
  GUU = "V", GCU = "A", GAU = "D", GGU = "G",
  GUC = "V", GCC = "A", GAC = "D", GGC = "G",
  GUA = "V", GCA = "A", GAA = "E", GGA = "G",
  GUG = "V", GCG = "A", GAG = "E", GGG = "G"
)

RNA -> Protein translasyonu

translate_rna_to_protein <- function(rna) {
  rna <- toupper(rna)
  codons <- unlist(strsplit(rna, "(?<=.{3})", perl=TRUE))
  protein <- sapply(codons, function(codon) codon_table[codon])
  protein <- protein[protein != "Stop"]
  return(paste(protein, collapse=""))
}

protein_sequence <- translate_rna_to_protein(rna_sequence)
cat("Protein Sequence: ", protein_sequence, "\n")

## Protein Sequence:  MAIVMGRKGAR

DNA dizisinde mutasyon ekleme

mutate_dna <- function(dna, position, new_base) {
  substr(dna, position, position) <- new_base
  return(dna)
}

Örnek mutasyon

mutated_dna <- mutate_dna(dna_sequence, 10, "A")
mutated_rna <- transcribe_dna_to_rna(mutated_dna)
mutated_protein <- translate_rna_to_protein(mutated_rna)

cat("Mutated DNA Sequence: ", mutated_dna, "\n")

## Mutated DNA Sequence:  ATGGCCATTATAATGGGCCGCTGAAAGGGTGCCCGATAG

cat("Mutated RNA Sequence: ", mutated_rna, "\n")

## Mutated RNA Sequence:  AUGGCCAUUAUAAUGGGCCGCUGAAAGGGUGCCCGAUAG

cat("Mutated Protein Sequence: ", mutated_protein, "\n")

## Mutated Protein Sequence:  MAIIMGRKGAR

Gerekli paketlerin yüklenmesi

library(ggplot2)

## Warning: package 'ggplot2' was built under R version 4.3.3

library(gridExtra)

## Warning: package 'gridExtra' was built under R version 4.3.3

DNA, RNA ve Protein dizilerini data frame’e dönüştürme

dna_df <- data.frame(Position = 1:nchar(dna_sequence), Base = strsplit(dna_sequence, NULL)[[1]])
rna_df <- data.frame(Position = 1:nchar(rna_sequence), Base = strsplit(rna_sequence, NULL)[[1]])
protein_df <- data.frame(Position = seq(1, nchar(protein_sequence) * 3, by = 3), AminoAcid = strsplit(protein_sequence, NULL)[[1]])

DNA grafiği

dna_plot <- ggplot(dna_df, aes(x = Position, y = 1, label = Base, color = Base)) +
  geom_text(size = 6) +
  scale_color_manual(values = c("A" = "red", "T" = "orange", "G" = "blue", "C" = "purple")) +
  theme_minimal() +
  labs(title = "DNA Sequence") +
  theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), axis.title.y = element_blank())

RNA grafiği

rna_plot <- ggplot(rna_df, aes(x = Position, y = 1, label = Base, color = Base)) +
  geom_text(size = 6) +
  scale_color_manual(values = c("A" = "red", "U" = "turquoise", "G" = "blue", "C" = "purple")) +
  theme_minimal() +
  labs(title = "RNA Sequence") +
  theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), axis.title.y = element_blank())

Protein grafiği

protein_plot <- ggplot(protein_df, aes(x = Position, y = 1, label = AminoAcid, color = AminoAcid)) +
  geom_text(size = 6) +
  scale_color_manual(values = rainbow(nchar(protein_sequence))) +
  theme_minimal() +
  labs(title = "Protein Sequence") +
  theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), axis.title.y = element_blank())

Grafiklerin birleştirilmesi

combined_plot <- grid.arrange(dna_plot, rna_plot, protein_plot, ncol = 1)

# Grafiklerin kaydedilmesi

ggsave("dna_rna_protein_plots.png", combined_plot, width = 10, height = 15, units = "in", dpi = 300)