01-BLAST-web-exercises.ipynb

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   "source": [
    "---\n",
    "typora-copy-images-to: ./\n",
    "sequence-fold: 80 xclip -o | tr -d \"\\n\" | fold -w80\n",
    "command-fold: 75 xclip -o | tr -d \"\\n\" | fold -sw75 | sed -e 's/$/\\\\/'\n",
    "last-update: April 2nd, 2018\n",
    "---\n",
    "\n",
    "# Web BLAST exercises\n",
    "\n",
    "by *alper yilmaz* for *GTU Bioinformatics Program Course*\n",
    "\n",
    "*2019-03-14* (PDF version of this document is accessible at `goo.gl/bhrkqQ` and html version is available at `https://goo.gl/siUoax`)\n",
    "\n",
    "\n",
    "> Please go over  [Guide to BLAST home and search pages](ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLASTGuide.pdf) and [BLAST Report description](ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_NewBLAST.pdf) guides before proceeding with exercises.\n",
    "\n",
    "## Question1\n",
    "\n",
    "If we align A and B (sequences are provided below) what would be the layout of the alignment?\n",
    "\n",
    "![Selection_339](images/Selection_339.png)\n",
    "\n",
    "Sequence for A"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [],
   "source": [
    ">A\n",
    "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTG\n",
    "GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC\n",
    "AGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT\n",
    "AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGG\n",
    "TAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG\n",
    "ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG\n",
    "GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT\n",
    "GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAA\n",
    "AACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA\n",
    "ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT\n",
    "GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTG\n",
    "ATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC\n",
    "TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTG\n",
    "CGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG\n",
    "CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT\n",
    "CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACAT\n",
    "GGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCG\n",
    "CCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG\n",
    "CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG"
   ]
  },
  {
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   "metadata": {},
   "source": [
    "<div style=\"page-break-after: always;\"></div>\n",
    "\n",
    "Sequence for B"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [],
   "source": [
    ">B\n",
    "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTG\n",
    "GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC\n",
    "AGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT\n",
    "AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGG\n",
    "TAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG\n",
    "ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG\n",
    "GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT\n",
    "GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAA\n",
    "AACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA\n",
    "ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCTACTCTGCTGCGGTGCTGGC\n",
    "TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCG\n",
    "ATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC\n",
    "ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCTCAAGCACCAGGTACGCTCAT\n",
    "TGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTG\n",
    "GTCCGGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG\n",
    "ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCA\n",
    "GGAAGAGTTCTACCTGGAAC"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!-- answer: c -->\n",
    "\n",
    "## Question2\n",
    "\n",
    "In which cases *query coverage* is 100% (more than one correct answer is accepted)\n",
    "\n",
    "![Selection_338](images/Selection_338.png)\n",
    "\n",
    "<!-- answer: a and c -->\n",
    "\n",
    "<div style=\"page-break-after: always;\"></div>\n",
    "\n",
    "## Question3\n",
    "\n",
    "The sequence below is used in the book \"*Jurassic Park THE LOST WORLD*\". Please use blastx to find the hidden message. (Hint: unaligned sequences)"
   ]
  },
  {
   "cell_type": "code",
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   "outputs": [],
   "source": [
    ">DinoDNA from THE LOST WORLD p. 135\n",
    "GAATTCCGGAAGCGAGCAAGAGATAAGTCCTGGCATCAGATACAGTTGGAGATAAGGACGGACGTGTGGCAGCTCCCGCA\n",
    "GAGGATTCACTGGAAGTGCATTACCTATCCCATGGGAGCCATGGAGTTCGTGGCGCTGGGGGGGCCGGATGCGGGCTCCC\n",
    "CCACTCCGTTCCCTGATGAAGCCGGAGCCTTCCTGGGGCTGGGGGGGGGCGAGAGGACGGAGGCGGGGGGGCTGCTGGCC\n",
    "TCCTACCCCCCCTCAGGCCGCGTGTCCCTGGTGCCGTGGGCAGACACGGGTACTTTGGGGACCCCCCAGTGGGTGCCGCC\n",
    "CGCCACCCAAATGGAGCCCCCCCACTACCTGGAGCTGCTGCAACCCCCCCGGGGCAGCCCCCCCCATCCCTCCTCCGGGC\n",
    "CCCTACTGCCACTCAGCAGCGGGCCCCCACCCTGCGAGGCCCGTGAGTGCGTCATGGCCAGGAAGAACTGCGGAGCGACG\n",
    "GCAACGCCGCTGTGGCGCCGGGACGGCACCGGGCATTACCTGTGCAACTGGGCCTCAGCCTGCGGGCTCTACCACCGCCT\n",
    "CAACGGCCAGAACCGCCCGCTCATCCGCCCCAAAAAGCGCCTGCTGGTGAGTAAGCGCGCAGGCACAGTGTGCAGCCACG\n",
    "AGCGTGAAAACTGCCAGACATCCACCACCACTCTGTGGCGTCGCAGCCCCATGGGGGACCCCGTCTGCAACAACATTCAC\n",
    "GCCTGCGGCCTCTACTACAAACTGCACCAAGTGAACCGCCCCCTCACGATGCGCAAAGACGGAATCCAAACCCGAAACCG\n",
    "CAAAGTTTCCTCCAAGGGTAAAAAGCGGCGCCCCCCGGGGGGGGGAAACCCCTCCGCCACCGCGGGAGGGGGCGCTCCTA\n",
    "TGGGGGGAGGGGGGGACCCCTCTATGCCCCCCCCGCCGCCCCCCCCGGCCGCCGCCCCCCCTCAAAGCGACGCTCTGTAC\n",
    "GCTCTCGGCCCCGTGGTCCTTTCGGGCCATTTTCTGCCCTTTGGAAACTCCGGAGGGTTTTTTGGGGGGGGGGCGGGGGG\n",
    "TTACACGGCCCCCCCGGGGCTGAGCCCGCAGATTTAAATAATAACTCTGACGTGGGCAAGTGGGCCTTGCTGAGAAGACA\n",
    "GTGTAACATAATAATTTGCACCTCGGCAATTGCAGAGGGTCGATCTCCACTTTGGACACAACAGGGCTACTCGGTAGGAC\n",
    "CAGATAAGCACTTTGCTCCCTGGACTGAAAAAGAAAGGATTTATCTGTTTGCTTCTTGCTGACAAATCCCTGTGAAAGGT\n",
    "AAAAGTCGGACACAGCAATCGATTATTTCTCGCCTGTGTGAAATTACTGTGAATATTGTAAATATATATATATATATATA\n",
    "TATATCTGTATAGAACAGCCTCGGAGGCGGCATGGACCCAGCGTAGATCATGCTGGATTTGTACTGCCGGAATTC"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Question4\n",
    "\n",
    "The peptide sequence below is translation of 4th exon of a Drosophilia gene. Use blastp and swissprot index to find out gene name."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "MSLTVEIVATKPYEGQKPGTSGLRKKVKVFTQPNYTENFVQAILEANGAALAGSTLVVGGDGRFYCKEAAELIVRLSAAN\n",
    "GVSKLLVGQNGILSTPAVSSLIRHNKALGGIVLTASHNPGGPENDFGIKFNCENGGPAPDAFTNHIYKITTEIKEYKLVR\n",
    "NLQIDISKVGVTSFDIAGKPFTVEVIDSVANYVRHMEEIFDFAKLKDFVSGKATGKPLKMRIDAMNGVTGSYVREIFLNR\n",
    "LGATESSVVHTTPLPDFGGLHPDPNLTYAKDLVDTVAQGDYDIGAAFDGDGDRNMIIGSKAFFVTPSDSLAVIAHYLEAI\n",
    "PYFQKNGVQGFARSMPTASAVDLVGRKLGKEVFEVPTGWKYFGNLMDAGRLCLCGEESFGTGSNHIREKDGIWAVLAWIS\n",
    "VMQHTGKGIEDILKQHWSVYGRNYFTRYDYEECASDPCNEMVATMEKTITAPEFVGKSYSSGGKTYKVKEADNFSYTDPV\n",
    "DKSVATKQGLRIVFEDGSRIVVRLSGTGSSGATVRLYIDSYEKENVLGQASVMLKPLIDIALEISQLPKFTGRNAPTVIT"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!-- PGM1(Phosphoglucomutase) -->\n",
    "\n",
    "<div style=\"page-break-after: always;\"></div>\n",
    "\n",
    "## Question5\n",
    "\n",
    "Below is the sequence of a HIV protein, please find out at which codon (nucleotide coordinate) the frameshift had taken place."
   ]
  },
  {
   "cell_type": "code",
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   "outputs": [],
   "source": [
    "ATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGCACCATGCTCCTTGGGTTGTTGATGATCCGTAGTGCTGC\n",
    "AGACCAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAAGAAGCAACCACCACTCCATTTTGTGCATCAGATG\n",
    "CTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACACGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTA\n",
    "GTATTGGCAAATGTGGCAGAAAATTTTAACATGTGGGATAATAACATGGTAGAACAGATGCATGAGGATATAATCAGTTT\n",
    "ATGGGATCAAAGCCTAAAGCCATGTGTTAAATTAACCCCACTCTGTGTTACTTTAAACTGCACTGATAAGATTAATAATA\n",
    "CCAAAACTACTCCTAATAATACCAGTACTACTCCCCCTACCACTGTTACTCCTACTAGTAATAGCAGCATGACAGGAGAA\n",
    "GGAGAAATAAAAAACTGCTCTTTCAATATCACCACAGCCATAAGAGATAAGGTGCAGAGAGGATATGCATTGTTTAGTAA\n",
    "ACTTTGATATAGTACCAATAGATAATGATAGAAATGATAGTACCAGCTATAGGTTGCTAAGTTGTAACACCTCAGTCATT\n",
    "ACACAAGCCTGTCCAAAGGTATCCTTTGAACCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTG\n",
    "TAACAATAAGACGTTCAGTGGAACAGGACCCTGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAATAG\n",
    "TATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGGGATAGTAATTAGATATGAAAATATCACAGACAATGCT\n",
    "AAAAGCATAATAATACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAATAATACAAGGAAAAGTATACC\n",
    "TATAGGACCAGGAAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGAAAAGCATATTGTAACATTAGTGGAG\n",
    "CAAAATGGAATAACACTTTAAAAAGGATAGCTTACAAATTAAAAGAACAATTTCCTAATAAAACAATAGTCTTTAAGCCC\n",
    "TCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAATTGTAGAGGGGAATTTTTCTACTGTAATACAACAAAACT\n",
    "GTTTGATAGTAGTTGGGATAATACTAATTTGAATAAAACTTGGAATAATACCTGGAATAAAAATAACTCTATCATACTTC\n",
    "CATGCAGAATAAAACAAATCATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCGAAGGACCACTT\n",
    "TACTGTTTATCAAATATTACAGGGCTAATTTTAACAAGAGATGGTGGGAACGAAACTGATGGGAACAACACTGATGGGAA\n",
    "TGAGACCTTCAGACCTGGAGGAGGGAATATGAGGGACAATTGGA"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!-- 564 -->\n",
    "\n",
    "## Question6\n",
    "\n",
    "Following sequence ([source](https://www.ncbi.nlm.nih.gov/Class/BLAST/blast_course.html)) belongs to a *C.elegans* gene. Please find its homologs in vertebrates. (Hint: use taxonomy report in results) \n",
    "\n",
    "```\n",
    ">C.elegans protein\n",
    "MFHPGMTSQPSTSNQMYYDPLYGAEQIVQCNPMDYHQANILCGMQYFNNSHNRYPLLPQMPPQFTNDHPYDFPNVPTIST\n",
    "LDEASSFNGFLIPSQPSSYNNNNISCVFTPTPCTSSQASSQPPPTPTVNPTPIPPNAGAVLTTAMDSCQQISHVLQCYQQ\n",
    "GGEDSDFVRKAIESLVKKLKDKRIELDALITAVTSNGKQPTGCVTIQRSLDGRLQVAGRKGVPHVVYARIWRWPKVSKNE\n",
    "LVKLVQCQTSSDHPDNICINPYHYERVVSNRITSADQSLHVENSPMKSEYLGDAGVIDSCSDWPNTPPDNNFNGGFAPDQ\n",
    "PQLVTPIISDIPIDLNQIYVPTPPQLLDNWCSIIYYELDTPIGETFKVSARDHGKVIVDGGMDPHGENEGRLCLGALSNV\n",
    "HRTEASEKARIHIGRGVELTAHADGNISITSNCKIFVRSGYLDYTHGSEYSSKAHRFTPNESSFTVFDIRWAYMQMLRRS\n",
    "RSSNEAVRAQAAAVAGYAPMSVMPAIMPDSGVDRMRRDFCTIAISFVKAWGDVYQRKTIKETPCWIEVTLHRPLQILDQL\n",
    "LKNSSQFGSS\n",
    "```"
   ]
  }
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