# #——包括= FALSE --------------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,评论 = "#>" ) ## ----------------------------------------------------------------------------- # (“idpr BiocManager:安装 ") ## ----------------------------------------------------------------------------- # devtools:: install_github(“wmm27 / idpr ") ## ----------------------------------------------------------------------------- 库(idpr ) ## ----------------------------------------------------------------------------- EDSSMat62 # #----------------------------------------------------------------------------- Disorder40 ## ----------------------------------------------------------------------------- Disorder85 ## ----------------------------------------------------------------------------- DUNMat ## ----------------------------------------------------------------------------- P53_MOUSE < - TP53Sequences[1]打印(P53_MOUSE) P53_HUMAN < - TP53Sequences[2]打印(P53_HUMAN) P53_GORILLA < - GorillaTP53打印(P53_GORILLA) # #----------------------------------------------------------------------------- library(Biostrings) data("BLOSUM62") #从Biostrings包中加载矩阵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, gapOpening = 19，gapExtension = 2)打印(HUMAN_GORILLA_EDSS_PSA ) ## ----------------------------------------------------------------------------- TP53_Sequences < - TP53Sequences打印(TP53_Sequences ) ## ----------------------------------------------------------------------------- 库(msa) BLOSUM_MSA < - msa (TP53_Sequences类型=“蛋白质”,substitutionMatrix = BLOSUM62 gapOpening = 10, gapExtension = 0.5)打印(BLOSUM_MSA,显示= "完成 ") ## ----------------------------------------------------------------------------- EDSS_MSA < - msa (TP53_Sequences类型=“蛋白质”,substitutionMatrix = EDSSMat62 gapOpening = 19日gapExtension = 2)打印(EDSS_MSA,显示= "完成 ") ## ---- 图一,fig.height = 4, fig.width = 6 -------------------------------------- EDSS_MSA_Tree < - msa:: msaConvert (EDSS_MSA类型=“seqinr:对齐”)d < - seqinr:: dist。align (EDSS_MSA_Tree， "identity") p53Tree <- ape::nj(d) plot(p53Tree， "id ")主要= " p53序列的系统发育树\ nAligned EDSSMat62 ") ## ---- 结果= " asis "---------------------------------------------------------- 引用(“Biostrings”)引用(msa)引文引用(“seqinr(“猿”) ") ## ----------------------------------------------------------------------------- R.version.string ## ----------------------------------------------------------------------------- as.data.frame (Sys.info ()) ## ----结果= " asis "---------------------------------------------------------- 引用()