3.02_GlobalAlignment.ipynb

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    "alphabet = ['A', 'C', 'G', 'T']\n",
    "score = [[0, 4, 2, 4, 8],\n",
    "         [4, 0, 4, 2, 8],\n",
    "         [2, 4, 0, 4, 8],\n",
    "         [4, 2, 4, 0, 8],\n",
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    "# converts from character to its offset in list alphabet\n",
    "alphabet.index('A')"
   ]
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    "alphabet.index('G')"
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   "source": [
    "# penalty associated with A (from X) mismatching with T (from Y)\n",
    "score[alphabet.index('A')][alphabet.index('T')]"
   ]
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   "source": [
    "# penalty associated with C (from X) being deleted in Y\n",
    "score[alphabet.index('C')][-1]"
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    "def globalAlignment(x, y):\n",
    "    # Create distance matrix\n",
    "    D = []\n",
    "    for i in range(len(x)+1):\n",
    "        D.append([0] * (len(y)+1))\n",
    "        \n",
    "    # Initialize first column\n",
    "    for i in range(1, len(x)+1):\n",
    "        D[i][0] = D[i-1][0] + score[alphabet.index(x[i-1])][-1]\n",
    "\n",
    "    # Initialize first row\n",
    "    for j in range(1,len(y)+1):\n",
    "        D[0][j] = D[0][j-1] + score[-1][alphabet.index(y[j-1])]\n",
    "        \n",
    "    # Fill rest of the matrix\n",
    "    for i in range(1, len(x)+1):\n",
    "        for j in range(1, len(y)+1):\n",
    "            distHor = D[i][j-1] + score[-1][alphabet.index(y[j-1])]\n",
    "            distVer = D[i-1][j] + score[alphabet.index(x[i-1])][-1]\n",
    "            distDiag = D[i-1][j-1] + score[alphabet.index(x[i-1])][alphabet.index(y[j-1])]\n",
    "            D[i][j] = min(distHor, distVer, distDiag)\n",
    "    \n",
    "    return D[-1][-1]  # return value in bottom right corner"
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     "text": [
      "12\n"
     ]
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   "source": [
    "x = 'TATGTCATGC'\n",
    "y = 'TATGGCAGC'\n",
    "print(globalAlignment(x,y))"
   ]
  }
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