# Author: Benben Miao

# Email: [email protected]

# Rversion: 4.2.0

# Date: 2023-02-25

# -> 0. Install and Library

# BiocManager::install("Biostrings")

library(Biostrings)

# <- 0. Install and Library

options(warn = 1)

# -> 1. File Read

file_path = "data/RevCom/RXAs-DNA.fasta"

seqType <- "DNA"

# ChoiceBox: "DNA", "RNA", "AminoAcid"

if (seqType == "DNA") {

seqs <- readDNAStringSet(file_path,

format = "fasta",

nrec = -1L,

skip = 0L,

seek.first.rec = FALSE,

use.names = TRUE,

with.qualities = FALSE)

} else if (seqType == "RNA") {

seqs <- readRNAStringSet(file_path,

format = "fasta",

nrec = -1L,

skip = 0L,

seek.first.rec = FALSE,

use.names = TRUE,

with.qualities = FALSE)

} else if (seqType == "AminoAcid") {

seqs <- readAAStringSet(file_path,

format = "fasta",

nrec = -1L,

skip = 0L,

seek.first.rec = FALSE,

use.names = TRUE,

with.qualities = FALSE)

}

# <- 1. File Read

# -> 2. Data Operation

alignType <- "global"

# ChoiceBox: "global", "local", "overlap", "global-local", "local-global"

scoreMatrix <- "BLOSUM62"

# ChoiceBox: "BLOSUM45", "BLOSUM50", "BLOSUM62", "BLOSUM80", "BLOSUM100", "PAM30", "PAM40", "PAM70", "PAM120", "PAM250"

gapOpening <- 10

# Slider: 10, 0, 100, 1

gapExtension <- 3

# Slider: 3, 0, 100, 1

res <- pairwiseAlignment(seqs[1],

seqs[2],

type = alignType, # "global", "local", "overlap", "global-local", "local-global"

# (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment

substitutionMatrix = scoreMatrix, # "BLOSUM45", "BLOSUM50", "BLOSUM62", "BLOSUM80", "BLOSUM100", "PAM30", "PAM40", "PAM70", "PAM120", "PAM250"

fuzzyMatrix = NULL,

gapOpening = gapOpening,

gapExtension = gapExtension,

scoreOnly = FALSE)

writePairwiseAlignments(res, file = "Results.txt",

Matrix = NA, block.width = 80)

# writeXStringSet(seqs2,

# filepath = "Results.fasta",

# append = FALSE,

# compress = FALSE,

# compression_level = NA,

# format = "fasta")

# write.table(as.data.frame(palindrome@ranges), file = "Results.txt",

# quote = F, sep = "\t", row.names = F)

# <- 2. Data Operation