blosum 0.1.0

data/lib/blosum.rb

@@ -0,0 +1,12 @@
+require "blosum/version"
+
+# BLOSUM matrices
+require "blosum/blosum45"
+require "blosum/blosum50"
+require "blosum/blosum62"
+require "blosum/blosum80"
+require "blosum/blosum90"
+
+module Blosum
+  class Error < StandardError; end
+end

data/lib/blosum/blosum45.rb

@@ -0,0 +1,679 @@
+module Blosum
+  BLOSUM45 = {
+    "A" => {
+      "A" =>  5,
+      "R" => -2,
+      "N" => -1,
+      "D" => -2,
+      "C" => -1,
+      "Q" => -1,
+      "E" => -1,
+      "G" =>  0,
+      "H" => -2,
+      "I" => -1,
+      "L" => -1,
+      "K" => -1,
+      "M" => -1,
+      "F" => -2,
+      "P" => -1,
+      "S" =>  1,
+      "T" =>  0,
+      "W" => -2,
+      "Y" => -2,
+      "V" =>  0,
+      "B" => -1,
+      "J" => -1,
+      "Z" => -1,
+      "X" => -1,
+      "*" => -5
+    },
+    "R" => {
+      "A" => -2,
+      "R" =>  7,
+      "N" =>  0,
+      "D" => -1,
+      "C" => -3,
+      "Q" =>  1,
+      "E" =>  0,
+      "G" => -2,
+      "H" =>  0,
+      "I" => -3,
+      "L" => -2,
+      "K" =>  3,
+      "M" => -1,
+      "F" => -2,
+      "P" => -2,
+      "S" => -1,
+      "T" => -1,
+      "W" => -2,
+      "Y" => -1,
+      "V" => -2,
+      "B" => -1,
+      "J" => -3,
+      "Z" =>  1,
+      "X" => -1,
+      "*" => -5
+    },
+    "N" => {
+      "A" => -1,
+      "R" =>  0,
+      "N" =>  6,
+      "D" =>  2,
+      "C" => -2,
+      "Q" =>  0,
+      "E" =>  0,
+      "G" =>  0,
+      "H" =>  1,
+      "I" => -2,
+      "L" => -3,
+      "K" =>  0,
+      "M" => -2,
+      "F" => -2,
+      "P" => -2,
+      "S" =>  1,
+      "T" =>  0,
+      "W" => -4,
+      "Y" => -2,
+      "V" => -3,
+      "B" =>  5,
+      "J" => -3,
+      "Z" =>  0,
+      "X" => -1,
+      "*" => -5
+    },
+    "D" => {
+      "A" => -2,
+      "R" => -1,
+      "N" =>  2,
+      "D" =>  7,
+      "C" => -3,
+      "Q" =>  0,
+      "E" =>  2,
+      "G" => -1,
+      "H" =>  0,
+      "I" => -4,
+      "L" => -3,
+      "K" =>  0,
+      "M" => -3,
+      "F" => -4,
+      "P" => -1,
+      "S" =>  0,
+      "T" => -1,
+      "W" => -4,
+      "Y" => -2,
+      "V" => -3,
+      "B" =>  6,
+      "J" => -3,
+      "Z" =>  1,
+      "X" => -1,
+      "*" => -5
+    },
+    "C" => {
+      "A" => -1,
+      "R" => -3,
+      "N" => -2,
+      "D" => -3,
+      "C" =>  12,
+      "Q" => -3,
+      "E" => -3,
+      "G" => -3,
+      "H" => -3,
+      "I" => -3,
+      "L" => -2,
+      "K" => -3,
+      "M" => -2,
+      "F" => -2,
+      "P" => -4,
+      "S" => -1,
+      "T" => -1,
+      "W" => -5,
+      "Y" => -3,
+      "V" => -1,
+      "B" => -2,
+      "J" => -2,
+      "Z" => -3,
+      "X" => -1,
+      "*" => -5
+    },
+    "Q" => {
+      "A" => -1,
+      "R" =>  1,
+      "N" =>  0,
+      "D" =>  0,
+      "C" => -3,
+      "Q" =>  6,
+      "E" =>  2,
+      "G" => -2,
+      "H" =>  1,
+      "I" => -2,
+      "L" => -2,
+      "K" =>  1,
+      "M" =>  0,
+      "F" => -4,
+      "P" => -1,
+      "S" =>  0,
+      "T" => -1,
+      "W" => -2,
+      "Y" => -1,
+      "V" => -3,
+      "B" =>  0,
+      "J" => -2,
+      "Z" =>  4,
+      "X" => -1,
+      "*" => -5
+    },
+    "E" => {
+      "A" => -1,
+      "R" =>  0,
+      "N" =>  0,
+      "D" =>  2,
+      "C" => -3,
+      "Q" =>  2,
+      "E" =>  6,
+      "G" => -2,
+      "H" =>  0,
+      "I" => -3,
+      "L" => -2,
+      "K" =>  1,
+      "M" => -2,
+      "F" => -3,
+      "P" =>  0,
+      "S" =>  0,
+      "T" => -1,
+      "W" => -3,
+      "Y" => -2,
+      "V" => -3,
+      "B" =>  1,
+      "J" => -3,
+      "Z" =>  5,
+      "X" => -1,
+      "*" => -5
+    },
+    "G" => {
+      "A" =>  0,
+      "R" => -2,
+      "N" =>  0,
+      "D" => -1,
+      "C" => -3,
+      "Q" => -2,
+      "E" => -2,
+      "G" =>  7,
+      "H" => -2,
+      "I" => -4,
+      "L" => -3,
+      "K" => -2,
+      "M" => -2,
+      "F" => -3,
+      "P" => -2,
+      "S" =>  0,
+      "T" => -2,
+      "W" => -2,
+      "Y" => -3,
+      "V" => -3,
+      "B" => -1,
+      "J" => -4,
+      "Z" => -2,
+      "X" => -1,
+      "*" => -5
+    },
+    "H" => {
+      "A" => -2,
+      "R" =>  0,
+      "N" =>  1,
+      "D" =>  0,
+      "C" => -3,
+      "Q" =>  1,
+      "E" =>  0,
+      "G" => -2,
+      "H" =>  10,
+      "I" => -3,
+      "L" => -2,
+      "K" => -1,
+      "M" =>  0,
+      "F" => -2,
+      "P" => -2,
+      "S" => -1,
+      "T" => -2,
+      "W" => -3,
+      "Y" =>  2,
+      "V" => -3,
+      "B" =>  0,
+      "J" => -2,
+      "Z" =>  0,
+      "X" => -1,
+      "*" => -5
+    },
+    "I" => {
+      "A" => -1,
+      "R" => -3,
+      "N" => -2,
+      "D" => -4,
+      "C" => -3,
+      "Q" => -2,
+      "E" => -3,
+      "G" => -4,
+      "H" => -3,
+      "I" =>  5,
+      "L" =>  2,
+      "K" => -3,
+      "M" =>  2,
+      "F" =>  0,
+      "P" => -2,
+      "S" => -2,
+      "T" => -1,
+      "W" => -2,
+      "Y" =>  0,
+      "V" =>  3,
+      "B" => -3,
+      "J" =>  4,
+      "Z" => -3,
+      "X" => -1,
+      "*" => -5
+    },
+    "L" => {
+      "A" => -1,
+      "R" => -2,
+      "N" => -3,
+      "D" => -3,
+      "C" => -2,
+      "Q" => -2,
+      "E" => -2,
+      "G" => -3,
+      "H" => -2,
+      "I" =>  2,
+      "L" =>  5,
+      "K" => -3,
+      "M" =>  2,
+      "F" =>  1,
+      "P" => -3,
+      "S" => -3,
+      "T" => -1,
+      "W" => -2,
+      "Y" =>  0,
+      "V" =>  1,
+      "B" => -3,
+      "J" =>  4,
+      "Z" => -2,
+      "X" => -1,
+      "*" => -5
+    },
+    "K" => {
+      "A" => -1,
+      "R" =>  3,
+      "N" =>  0,
+      "D" =>  0,
+      "C" => -3,
+      "Q" =>  1,
+      "E" =>  1,
+      "G" => -2,
+      "H" => -1,
+      "I" => -3,
+      "L" => -3,
+      "K" =>  5,
+      "M" => -1,
+      "F" => -3,
+      "P" => -1,
+      "S" => -1,
+      "T" => -1,
+      "W" => -2,
+      "Y" => -1,
+      "V" => -2,
+      "B" =>  0,
+      "J" => -3,
+      "Z" =>  1,
+      "X" => -1,
+      "*" => -5
+    },
+    "M" => {
+      "A" => -1,
+      "R" => -1,
+      "N" => -2,
+      "D" => -3,
+      "C" => -2,
+      "Q" =>  0,
+      "E" => -2,
+      "G" => -2,
+      "H" =>  0,
+      "I" =>  2,
+      "L" =>  2,
+      "K" => -1,
+      "M" =>  6,
+      "F" =>  0,
+      "P" => -2,
+      "S" => -2,
+      "T" => -1,
+      "W" => -2,
+      "Y" =>  0,
+      "V" =>  1,
+      "B" => -2,
+      "J" =>  2,
+      "Z" => -1,
+      "X" => -1,
+      "*" => -5
+    },
+    "F" => {
+      "A" => -2,
+      "R" => -2,
+      "N" => -2,
+      "D" => -4,
+      "C" => -2,
+      "Q" => -4,
+      "E" => -3,
+      "G" => -3,
+      "H" => -2,
+      "I" =>  0,
+      "L" =>  1,
+      "K" => -3,
+      "M" =>  0,
+      "F" =>  8,
+      "P" => -3,
+      "S" => -2,
+      "T" => -1,
+      "W" =>  1,
+      "Y" =>  3,
+      "V" =>  0,
+      "B" => -3,
+      "J" =>  1,
+      "Z" => -3,
+      "X" => -1,
+      "*" => -5
+    },
+    "P" => {
+      "A" => -1,
+      "R" => -2,
+      "N" => -2,
+      "D" => -1,
+      "C" => -4,
+      "Q" => -1,
+      "E" =>  0,
+      "G" => -2,
+      "H" => -2,
+      "I" => -2,
+      "L" => -3,
+      "K" => -1,
+      "M" => -2,
+      "F" => -3,
+      "P" =>  9,
+      "S" => -1,
+      "T" => -1,
+      "W" => -3,
+      "Y" => -3,
+      "V" => -3,
+      "B" => -2,
+      "J" => -3,
+      "Z" => -1,
+      "X" => -1,
+      "*" => -5
+    },
+    "S" => {
+      "A" =>  1,
+      "R" => -1,
+      "N" =>  1,
+      "D" =>  0,
+      "C" => -1,
+      "Q" =>  0,
+      "E" =>  0,
+      "G" =>  0,
+      "H" => -1,
+      "I" => -2,
+      "L" => -3,
+      "K" => -1,
+      "M" => -2,
+      "F" => -2,
+      "P" => -1,
+      "S" =>  4,
+      "T" =>  2,
+      "W" => -4,
+      "Y" => -2,
+      "V" => -1,
+      "B" =>  0,
+      "J" => -2,
+      "Z" =>  0,
+      "X" => -1,
+      "*" => -5
+    },
+    "T" => {
+      "A" =>  0,
+      "R" => -1,
+      "N" =>  0,
+      "D" => -1,
+      "C" => -1,
+      "Q" => -1,
+      "E" => -1,
+      "G" => -2,
+      "H" => -2,
+      "I" => -1,
+      "L" => -1,
+      "K" => -1,
+      "M" => -1,
+      "F" => -1,
+      "P" => -1,
+      "S" =>  2,
+      "T" =>  5,
+      "W" => -3,
+      "Y" => -1,
+      "V" =>  0,
+      "B" =>  0,
+      "J" => -1,
+      "Z" => -1,
+      "X" => -1,
+      "*" => -5
+    },
+    "W" => {
+      "A" => -2,
+      "R" => -2,
+      "N" => -4,
+      "D" => -4,
+      "C" => -5,
+      "Q" => -2,
+      "E" => -3,
+      "G" => -2,
+      "H" => -3,
+      "I" => -2,
+      "L" => -2,
+      "K" => -2,
+      "M" => -2,
+      "F" =>  1,
+      "P" => -3,
+      "S" => -4,
+      "T" => -3,
+      "W" =>  15,
+      "Y" =>  3,
+      "V" => -3,
+      "B" => -4,
+      "J" => -2,
+      "Z" => -2,
+      "X" => -1,
+      "*" => -5
+    },
+    "Y" => {
+      "A" => -2,
+      "R" => -1,
+      "N" => -2,
+      "D" => -2,
+      "C" => -3,
+      "Q" => -1,
+      "E" => -2,
+      "G" => -3,
+      "H" =>  2,
+      "I" =>  0,
+      "L" =>  0,
+      "K" => -1,
+      "M" =>  0,
+      "F" =>  3,
+      "P" => -3,
+      "S" => -2,
+      "T" => -1,
+      "W" =>  3,
+      "Y" =>  8,
+      "V" => -1,
+      "B" => -2,
+      "J" =>  0,
+      "Z" => -2,
+      "X" => -1,
+      "*" => -5
+    },
+    "V" => {
+      "A" =>  0,
+      "R" => -2,
+      "N" => -3,
+      "D" => -3,
+      "C" => -1,
+      "Q" => -3,
+      "E" => -3,
+      "G" => -3,
+      "H" => -3,
+      "I" =>  3,
+      "L" =>  1,
+      "K" => -2,
+      "M" =>  1,
+      "F" =>  0,
+      "P" => -3,
+      "S" => -1,
+      "T" =>  0,
+      "W" => -3,
+      "Y" => -1,
+      "V" =>  5,
+      "B" => -3,
+      "J" =>  2,
+      "Z" => -3,
+      "X" => -1,
+      "*" => -5
+    },
+    "B" => {
+      "A" => -1,
+      "R" => -1,
+      "N" =>  5,
+      "D" =>  6,
+      "C" => -2,
+      "Q" =>  0,
+      "E" =>  1,
+      "G" => -1,
+      "H" =>  0,
+      "I" => -3,
+      "L" => -3,
+      "K" =>  0,
+      "M" => -2,
+      "F" => -3,
+      "P" => -2,
+      "S" =>  0,
+      "T" =>  0,
+      "W" => -4,
+      "Y" => -2,
+      "V" => -3,
+      "B" =>  5,
+      "J" => -3,
+      "Z" =>  1,
+      "X" => -1,
+      "*" => -5
+    },
+    "J" => {
+      "A" => -1,
+      "R" => -3,
+      "N" => -3,
+      "D" => -3,
+      "C" => -2,
+      "Q" => -2,
+      "E" => -3,
+      "G" => -4,
+      "H" => -2,
+      "I" =>  4,
+      "L" =>  4,
+      "K" => -3,
+      "M" =>  2,
+      "F" =>  1,
+      "P" => -3,
+      "S" => -2,
+      "T" => -1,
+      "W" => -2,
+      "Y" =>  0,
+      "V" =>  2,
+      "B" => -3,
+      "J" =>  4,
+      "Z" => -2,
+      "X" => -1,
+      "*" => -5
+    },
+    "Z" => {
+      "A" => -1,
+      "R" =>  1,
+      "N" =>  0,
+      "D" =>  1,
+      "C" => -3,
+      "Q" =>  4,
+      "E" =>  5,
+      "G" => -2,
+      "H" =>  0,
+      "I" => -3,
+      "L" => -2,
+      "K" =>  1,
+      "M" => -1,
+      "F" => -3,
+      "P" => -1,
+      "S" =>  0,
+      "T" => -1,
+      "W" => -2,
+      "Y" => -2,
+      "V" => -3,
+      "B" =>  1,
+      "J" => -2,
+      "Z" =>  5,
+      "X" => -1,
+      "*" => -5
+    },
+    "X" => {
+      "A" => -1,
+      "R" => -1,
+      "N" => -1,
+      "D" => -1,
+      "C" => -1,
+      "Q" => -1,
+      "E" => -1,
+      "G" => -1,
+      "H" => -1,
+      "I" => -1,
+      "L" => -1,
+      "K" => -1,
+      "M" => -1,
+      "F" => -1,
+      "P" => -1,
+      "S" => -1,
+      "T" => -1,
+      "W" => -1,
+      "Y" => -1,
+      "V" => -1,
+      "B" => -1,
+      "J" => -1,
+      "Z" => -1,
+      "X" => -1,
+      "*" => -5
+    },
+    "*" => {
+      "A" => -5,
+      "R" => -5,
+      "N" => -5,
+      "D" => -5,
+      "C" => -5,
+      "Q" => -5,
+      "E" => -5,
+      "G" => -5,
+      "H" => -5,
+      "I" => -5,
+      "L" => -5,
+      "K" => -5,
+      "M" => -5,
+      "F" => -5,
+      "P" => -5,
+      "S" => -5,
+      "T" => -5,
+      "W" => -5,
+      "Y" => -5,
+      "V" => -5,
+      "B" => -5,
+      "J" => -5,
+      "Z" => -5,
+      "X" => -5,
+      "*" =>  1
+    }
+  }
+end