Question

我正在尝试从R中的BLOSUM62创建一个矩阵。

library(Biostrings)

seq_test <- c("PAWHEAE", "HEAGAWGHEE", "CAWEKDRRTEAFF", "CASSLVFGQGDNIQYF")

aligned <- pairwiseAlignment(seq_test, seq_test, substitutionMatrix="BLOSUM62")

score(aligned)
#44 62 76 86

它只是将每个序列与自身进行比较。我想让每个序列循环并比较整个序列列表，创建一个4x4矩阵。它看起来更像是这样：

44  -7 -23 -52
-7  62 -34 -40
-23 -34  76 -13
-52 -40 -13  86

Answer 1

创建所有组合然后比较：

#all combos
seq1 <- expand.grid(seq_test, seq_test)

#compare, convert to matrix
matrix(score(pairwiseAlignment(seq1$Var1, seq1$Var2,
                               substitutionMatrix = "BLOSUM62")),
       nrow = length(seq_test))
#      [,1] [,2] [,3] [,4]
# [1,]   44   -7  -23  -52
# [2,]   -7   62  -34  -40
# [3,]  -23  -34   76  -13
# [4,]  -52  -40  -13   86

或循环遍历向量：

sapply(seq_test, function(i){
  sapply(seq_test, function(j){
    score(pairwiseAlignment(i, j, substitutionMatrix = "BLOSUM62"))
          })
  })

#                  PAWHEAE HEAGAWGHEE CAWEKDRRTEAFF CASSLVFGQGDNIQYF
# PAWHEAE               44         -7           -23              -52
# HEAGAWGHEE            -7         62           -34              -40
# CAWEKDRRTEAFF        -23        -34            76              -13
# CASSLVFGQGDNIQYF     -52        -40           -13               86

从biostrings成对对齐BLOSUM创建矩阵

1 个答案: