library(seqinr)
library(Biostrings)
######################
#carregando a sequência de um arquivo fasta
#O arquivo deve conter somente 1 sequência
#para carregar uma sequencia o endereço deve ser trocado para onde o arquivo está
minhaSeqs as.string = TRUE, seqtype = “DNA”)[[1]]
minhaSeqs
minhaSeqs
######################
#Alinhamento global DNA
sigma sigma
s1 <- “GAATTC”
s2 <- “GATTA”
globalAligns1s2 gapExtension = -8, scoreOnly = FALSE)
globalAligns1s2
######################
#Alinhamento global proteína
data(BLOSUM50)
BLOSUM50
s3 <- “PAWHEAE”
s4 <- “HEAGAWGHEE”
globalAligns gapExtension = -8, scoreOnly = FALSE)
globalAligns
printPairwiseAlignment(globalAligns, 60)
######################
#Alinhamento local
localAlign substitutionMatrix = sigma, gapOpening = -2, gapExtension = -8, scoreOnly = FALSE, type=”local”)
localAlign
printPairwiseAlignment(localAlign, 60)
######################
#funcão para vizualizar alinhamentos
printPairwiseAlignment {
require(Biostrings)
seq1aln seq2aln alnlen starts n seq1alnresidues seq2alnresidues for (i in 1:n) {
chunkseq1aln chunkseq2aln
gaps1
gaps2
seq1alnresidues
seq2alnresidues if (returnlist == ‘FALSE’)
{
print(paste(chunkseq1aln,seq1alnresidues))
print(paste(chunkseq2aln,seq2alnresidues))
print(paste(‘ ‘))
}
}
if (returnlist == ‘TRUE’)
{
vector1 vector2 mylist return(mylist)
}
}
#carregando a biblioteca
library(Biostrings)
#montando matriz de substituição de DNA
matriz_subs #imprime a matriz de substituição
matriz_subs # Print out the matrix
seq1
seq2
alinhamento_DNA gapExtension = -2, scoreOnly = FALSE)
#alinhamento
alinhamento_DNA1
#alinhamento global
seq3
seq4
alinhamento_DNA_global gapExtension = -2, scoreOnly = FALSE, type = “global”)
#alinhamento
alinhamento_DNA_global
#alinhamento local
seq3
seq4
alinhamento_DNA_local gapExtension = -2, scoreOnly = FALSE, type = “local”)
#alinhamento
alinhamento_DNA_local
#alinhamento de Proteína
#acessando a matriz de proteína BLOSUM
#comparar a penalidade de troca dos aminoácidos
# entre as matrizes
#carregando a matriz BLOSUM45
data(“BLOSUM45″)
BLOSUM45
#carregando a matriz BLOSUM80
data(“BLOSUM80″)
BLOSUM45
seq3
seq4
alinhamento_PROT gapExtension = -8, scoreOnly = FALSE)
alinhamento_PROT
#carregando sequencias dos bancos
library(“seqinr”)
choosebank(“swissprot”)
lepra vetor_lepra_PROT ulcera vetor_ulcera_PROT closebank()
#transformando o vetor em string (sequencia)
lepra_PROT ulcera_PROT
#transformando minuscula para maiuscula
lepra_PROT ulcera_PROT
alinhamento_lepra_ucera substitutionMatrix = “BLOSUM50″, gapOpening = -2,
gapExtension = -8, scoreOnly = FALSE)
alinhamento_lepra_ucera
#funcao
printPairwiseAlignment {
require(Biostrings) # This function requires the Biostrings package
seq1aln seq2aln alnlen starts n seq1alnresidues seq2alnresidues for (i in 1:n) {
chunkseq1aln chunkseq2aln # Find out how many gaps there are in chunkseq1aln:
gaps1 # Find out how many gaps there are in chunkseq2aln:
gaps2 # Calculate how many residues of the first sequence we have printed so far in the alignment:
seq1alnresidues # Calculate how many residues of the second sequence we have printed so far in the alignment:
seq2alnresidues if (returnlist == ‘FALSE’)
{
print(paste(chunkseq1aln,seq1alnresidues))
print(paste(chunkseq2aln,seq2alnresidues))
print(paste(‘ ‘))
}
}
if (returnlist == ‘TRUE’)
{
vector1 vector2 mylist return(mylist)
}
}
printPairwiseAlignment(alignment = alinhamento_lepra_ucera, 60)
#funcao
printPairwiseAlignment {
require(Biostrings) # This function requires the Biostrings package
seq1aln seq2aln alnlen starts n seq1alnresidues seq2alnresidues for (i in 1:n) {
chunkseq1aln chunkseq2aln # Find out how many gaps there are in chunkseq1aln:
gaps1 # Find out how many gaps there are in chunkseq2aln:
gaps2 # Calculate how many residues of the first sequence we have printed so far in the alignment:
seq1alnresidues # Calculate how many residues of the second sequence we have printed so far in the alignment:
seq2alnresidues if (returnlist == ‘FALSE’)
{
print(paste(chunkseq1aln,seq1alnresidues))
print(paste(chunkseq2aln,seq2alnresidues))
print(paste(‘ ‘))
}
}
if (returnlist == ‘TRUE’)
{
vector1 vector2 mylist return(mylist)
}
}