## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----------------------------------------------------------------------------- #BiocManager::install("idpr") ## ----------------------------------------------------------------------------- #devtools::install_github("wmm27/idpr") ## ----------------------------------------------------------------------------- library(idpr) ## ----------------------------------------------------------------------------- EDSSMat62 ## ----------------------------------------------------------------------------- Disorder40 ## ----------------------------------------------------------------------------- Disorder85 ## ----------------------------------------------------------------------------- DUNMat ## ----------------------------------------------------------------------------- P53_MOUSE <- TP53Sequences[1] print(P53_MOUSE) P53_HUMAN <- TP53Sequences[2] print(P53_HUMAN) P53_GORILLA <- GorillaTP53 print(P53_GORILLA) ## ----------------------------------------------------------------------------- library(Biostrings) data("BLOSUM62") #loads the matrix from the Biostrings package HUMAN_MOUSE_BLOSUM_PSA <- pairwiseAlignment(P53_MOUSE, P53_HUMAN, substitutionMatrix = BLOSUM62, gapOpening = 10, gapExtension = 0.5) print(HUMAN_MOUSE_BLOSUM_PSA) HUMAN_GORILLA_BLOSUM_PSA <- pairwiseAlignment(P53_GORILLA, P53_HUMAN, substitutionMatrix = BLOSUM62, gapOpening = 10, gapExtension = 0.5) print(HUMAN_GORILLA_BLOSUM_PSA) ## ----------------------------------------------------------------------------- HUMAN_MOUSE_EDSS_PSA <- pairwiseAlignment(P53_MOUSE, P53_HUMAN, substitutionMatrix = EDSSMat62, gapOpening = 19, gapExtension = 2) print(HUMAN_MOUSE_EDSS_PSA) HUMAN_GORILLA_EDSS_PSA <- pairwiseAlignment(P53_GORILLA, P53_HUMAN, substitutionMatrix = EDSSMat62, gapOpening = 19, gapExtension = 2) print(HUMAN_GORILLA_EDSS_PSA) ## ----------------------------------------------------------------------------- TP53_Sequences <- TP53Sequences print(TP53_Sequences) ## ----------------------------------------------------------------------------- library(msa) BLOSUM_MSA <- msa(TP53_Sequences, type = "protein", substitutionMatrix = BLOSUM62, gapOpening = 10, gapExtension = 0.5) print(BLOSUM_MSA, show="complete") ## ----------------------------------------------------------------------------- EDSS_MSA <- msa(TP53_Sequences, type = "protein", substitutionMatrix = EDSSMat62, gapOpening = 19, gapExtension = 2) print(EDSS_MSA, show="complete") ## ----fig1, fig.height = 4, fig.width = 6-------------------------------------- EDSS_MSA_Tree <- msa::msaConvert(EDSS_MSA, type="seqinr::alignment") d <- seqinr::dist.alignment(EDSS_MSA_Tree, "identity") p53Tree <- ape::nj(d) plot(p53Tree, main="Phylogenetic Tree of p53 Sequences\nAligned with EDSSMat62") ## ---- results="asis"---------------------------------------------------------- citation("Biostrings") citation("msa") citation("ape") citation("seqinr") ## ----------------------------------------------------------------------------- R.version.string ## ----------------------------------------------------------------------------- as.data.frame(Sys.info()) ## ---- results="asis"---------------------------------------------------------- citation()