20230421 Finding a Motif in DNA.ipynb

{
 "cells": [
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   "cell_type": "code",
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   "id": "ac33138d",
   "metadata": {},
   "outputs": [],
   "source": [
    "def find_motif(seq,motif_seq):\n",
    "    if len(seq)<len(motif_seq):\n",
    "        raise ValueError(\"seq too short\")\n",
    "    match_list=[]\n",
    "    for i in range(len(seq)-len(motif_seq)+1):\n",
    "        if seq[i:i+len(motif_seq)]==motif_seq:\n",
    "            match_list.append(i+1)\n",
    "    \n",
    "    for element in match_list:\n",
    "        print(element,end=\" \")\n",
    "\n",
    "            \n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "3e173b49",
   "metadata": {},
   "outputs": [],
   "source": [
    "seq = \"GGGCTGACTAAAGTAACGCGCTTAAGTAACGAAGTAACGCCCTTAGTAACGAGTAACGCAAGTAACGCTCGCAGTAACGTAAGTAACGGTGAGAGAGTAACGAGTAACGCAGTAACGCGAAGTAACGAGTAACGTAGAGTAACGCTGGTTGGAGTAACGCAGTAACGCCAACGAGTAACGGGTGAGTAACGAGTAACGAGTAACGAGTAACGCCCACTGGACAGTAACGAGTAACGCAGTAACGGTGGAGTAACGAAAAGTAACGAGTAACGGTAGGAGTAACGATAGTAACGGTCTTGAAGTAACGACAGTAACGAGTAACGGAGTAACGTAAGTAACGGCAGTAACGAGTAACGGAGTAACGAAAAGTAACGAGTAACGCAAGTAACGGTAGTAACGTGAGTAACGTAGTAACGAAGTAACGATAGTAACGAGTAACGGCAGTAACGTTCCAGTAACGATGAAAGTAACGGTCAGTAACGTTGAAGGTCAGTAACGCCATCAAGTAACGTCAGTAACGCAGTAACGAGTAACGAAGTAACGAAGTAACGGCAGTAACGAAAGTAACGTAGAGTAACGTCCGAAGTAACGCCAGTAACGGGACGTAGTAACGGAAGTAACGAAAGTAACGTTAAGGAAGTAACGTAGTAACGCAGTAACGAGTAGTAACGAGCCATATTTTGATGCGATCGAGTAACGTAAGTAACGACAGTAACGGAGGATAGTAACGAGTAACGAGTAACGGGAGTAACGGTAGGCTAAGTAACGAGTAACGCAAAGTAACGTGACGATACATTCCGTTAGTAACGTACAGTAACGATGAGCGCGAGTAACGCATCAATAGTAACGGAGTAACGATAGTAACGTAGTAACGGGAGTAACGACAGTAACGACTTAT\"\n",
    "motif_seq = \"AGTAACGAG\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8c7360d7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "45 96 121 185 192 199 223 259 310 343 368 427 522 655 665 724 731 762 "
     ]
    }
   ],
   "source": [
    "find_motif(seq,motif_seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "50aca3f8",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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