Finalizing EMBOSS pairwise alignment with influenza

CY030230.1.fasta

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+>ENA|CY030230|CY030230.1 Influenza A virus (A/Brisbane/59/2007(H1N1)) segment 4 sequence.
+AGCAAAAGCAGGGGATAATAAAAACAACCAGAATGAAAGTAAAACTACTGGTCCTGTTAT
+GCACATTTACAGCTACATATGCAGACACAATATGTATAGGCTACCATGCTAACAACTCGA
+CCGACACTGTTGACACAGTACTTGAAAAGAATGTGACAGTGACACACTCTGTCAACCTGC
+TTGAGAACAGTCACAATGGAAAACTATGTCTATTAAAAGGAATAGCCCCACTACAATTGG
+GTAATTGCAGCGTTGCCGGGTGGATCTTAGGAAACCCAGAATGCGAATTACTGATTTCCA
+AGGAGTCATGGTCCTACATTGTAGAAAAACCAAATCCTGAGAATGGAACATGTTACCCAG
+GGCATTTCGCTGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCTTCATTTGAGA
+GGTTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGTGTCAG
+CATCATGCTCCCATAATGGGGAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGGGA
+AGAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGCAAACAACAAAGAAAAAGAAGTCC
+TTGTACTATGGGGTGTTCATCACCCGCCAAACATAGGTGACCAAAAGGCCCTCTATCATA
+CAGAAAATGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAAATTCACCCCAGAAA
+TAGCCAAAAGACCCAAAGTAAGAGATCAAGAAGGAAGAATCAATTACTACTGGACTCTGC
+TTGAACCCGGGGATACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCAAGATATG
+CTTTCGCACTGAGTAGAGGCTTTGGATCAGGAATCATCAACTCAAATGCACCAATGGATA
+AATGTGATGCGAAGTGCCAAACACCTCAGGGAGCTATAAACAGCAGTCTTCCTTTCCAGA
+ACGTACACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTGCAAAATTAAGGA
+TGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTG
+CCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGTTGGTATGGTTATCATCATC
+AGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGCACACAAAATGCCATTAATG
+GGATTACAAACAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCAGTGG
+GCAAAGAATTCAACAAATTGGAAAGAAGGATGGAAAACTTGAATAAAAAAGTTGATGATG
+GGTTTATAGACATTTGGACATATAATGCAGAACTGTTGGTTCTACTGGAAAATGAAAGGA
+CTTTGGATTTCCATGACTCCAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAGTTAA
+AGAATAATGCTAAAGAAATAGGAAATGGGTGTTTTGAATTCTATCACAAGTGTAACGATG
+AATGCATGGAGAGTGTAAAGAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAA
+AGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTC
+TGGCGATCTACTCAACAGTCGCCAGTTCTCTGGTTCTTTTGGTCTCCCTGGGGGCAATCA
+GCTTCTGGATGTGTTCCAATGGGTCTTTACAGTGTAGAATATGCATCTAAGACCAGAATT
+TCAGAAATATAAGGAAAAACA

FJ969540.1.fasta

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+>ENA|FJ969540|FJ969540.1 Influenza A virus (A/California/07/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds.
+ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTA
+TGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAAT
+GTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAA
+CTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGA
+AATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCT
+AGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAG
+CAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGG
+CCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGC
+TTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAA
+TCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCT
+ACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCA
+TCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGRTCRA
+GAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAA
+GCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCT
+GGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAG
+GGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGT
+CCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCT
+ATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGG
+ATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCC
+GACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATT
+GAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGA
+ATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCC
+GAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAG
+AACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGC
+TGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACT
+TATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTA
+AAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCA
+TTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTA
+CAGTGTAGAATATGTATTTAA

Schrick-Noah_CS-6643_Lab-8.R

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+# Lab 8 for the University of Tulsa's CS-6643 Bioinformatics Course
+# Pairwise Sequence Alignment
+# Professor: Dr. McKinney, Fall 2022
+# Noah L. Schrick - 1492657
+
+## Set Working Directory to file directory - RStudio approach
+setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
+
+#### Part A: EMBOSS pairwise alignment server and influenza
+## Load associated supportive libraries
+if (!require("seqinr")) install.packages("seqinr")
+library(seqinr)
+
+## Load in the fasta file
+fasta2vec <- function(fasta.file){
+  if (!require("seqinr")) install.packages("seqinr")
+  library(seqinr)
+  fasta <- read.fasta(file=fasta.file, as.string= TRUE)
+  fasta.string <- fasta[[1]][1]
+  fasta.list <- strsplit(fasta.string,"")
+  fasta.vec <- unlist(fasta.list)
+}
+
+h1n1.Cali.dna.vec <- fasta2vec("FJ969540.1.fasta")
+h1n1.Bris.dna.vec <- fasta2vec("CY030230.1.fasta")
+
+## Convert DNA seq into amino acid seq
+h1n1.Cali.aa.vec<-seqinr::translate(h1n1.Cali.dna.vec)
+h1n1.Cali.aa.table<-table(h1n1.Cali.aa.vec) # aa count table
+
+## Create dotchart of amino acid freqs
+# sort the table (smallest to largest)
+h1n1.Cali.aa.sortedtable <-h1n1.Cali.aa.table[order(h1n1.Cali.aa.table)]
+# convert the AA table names to 3-letter code
+# You can ignore the warning or remove the offending letters from
+# the table
+names(h1n1.Cali.aa.sortedtable)<-aaa(names(h1n1.Cali.aa.sortedtable)) 
+dotchart(h1n1.Cali.aa.sortedtable)
+
+# Repeating for Brisbane and accounting for shift in start codon
+h1n1.Bris.aa.vec <- seqinr::translate(h1n1.Bris.dna.vec)
+h1n1.Bris.aa.vec <- h1n1.Bris.aa.vec[-seq(1, match('M', h1n1.Bris.aa.vec)-1)]
+
+h1n1.Bris.aa.table<-table(h1n1.Bris.aa.vec) # aa count table
+h1n1.Bris.aa.sortedtable <-h1n1.Bris.aa.table[order(h1n1.Bris.aa.table)]
+
+names(h1n1.Bris.aa.sortedtable)<-aaa(names(h1n1.Bris.aa.sortedtable)) 
+dotchart(h1n1.Bris.aa.sortedtable)
+paste(h1n1.Bris.aa.vec,collapse="",sep="")
+# 
+