{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# RNA-Puzzle 18"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Init the library and needed functions."
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"import nglview\n",
"import rna_pdb_tools.Seq as Seq\n",
"import rna_pdb_tools.BlastPDB\n",
"from rna_pdb_tools.BlastPDB import BlastPDB\n",
"reload(rna_pdb_tools.BlastPDB);\n",
"reload(Seq);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Create a RNASeqence object."
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG\n"
]
}
],
"source": [
"seq = Seq.RNASequence(\"GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG\")\n",
"print(seq)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Secondary structure prediction"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
">rna_seq\n",
"GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG\n",
"(((((((((.(((((...)))))(((((((.....)))))))...)))))..)))).(((((....))))) (-33.10)\n"
]
}
],
"source": [
"print(seq.predict_ss())"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
">rna_seq [100]\n",
"GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG -33.10 1.00\n",
"(((((((((.((((.....))))(((((((.....)))))))...)))))..)))).(((((....))))) -32.40\n",
"(((((((((.(((((...)))))(((((((.....)))))))...)))))..)))).(((((....))))) -33.10\n",
"(((((((((((((....)))).((((((((.....))))))))..)))))..)))).(((((....))))) -32.30\n",
"\n"
]
}
],
"source": [
"print(seq.predict_ss(method='RNAsubopt'))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print(seq.predict_ss(method='ipknot'))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# PDB Blast search"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"BLAST Search Results\n",
"\n",
"\n",
"BLASTN 2.2.18 [Mar-02-2008]\n",
"\n",
"\n",
"Reference:\n",
"Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, \n",
"Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), \n",
"\"Gapped BLAST and PSI-BLAST: a new generation of protein database search\n",
"programs\", Nucleic Acids Res. 25:3389-3402.\n",
"\n",
"Query= UNKNOWN_SEQUENCE\n",
" (71 letters)\n",
"\n",
"Database: pdb_nucleotide \n",
" 19,357 sequences; 3,678,086 total letters\n",
"\n",
"Searching..................................................done\n",
"\n",
"\n",
"\n",
"\n",
" Score E\n",
"Sequences producing significant alignments: (bits) Value\n",
"\n",
"5TPY:1:A|pdbid|entity|chain(s)|sequence 105 3e-24\n",
"4PQV:1:A|pdbid|entity|chain(s)|sequence 34 0.010\n",
"\n",
"\n",
">5TPY:1:A|pdbid|entity|chain(s)|sequence\n",
" Length = 71\n",
"\n",
" Score = 105 bits (53), Expect = 3e-24\n",
" Identities = 53/53 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 1 gggtcaggccggcgaaagtcgccacagtttggggaaagctgtgcagcctgtaa 53\n",
" |||||||||||||||||||||||||||||||||||||||||||||||||||||\n",
"Sbjct: 1 gggtcaggccggcgaaagtcgccacagtttggggaaagctgtgcagcctgtaa 53\n",
"\n",
"\n",
"\n",
"\n",
">4PQV:1:A|pdbid|entity|chain(s)|sequence\n",
" Length = 68\n",
"\n",
" Score = 34.2 bits (17), Expect = 0.010\n",
" Identities = 23/25 (92%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 1 gggtcaggccggcgaaagtcgccac 25\n",
" ||||||| ||||||||||||||||\n",
"Sbjct: 1 gggtcagatcggcgaaagtcgccac 25\n",
"\n",
"\n",
"\n",
"\n",
" Database: pdb_nucleotide\n",
" Posted date: Sep 28, 2018 10:56 PM\n",
" Number of letters in database: 3,678,086\n",
" Number of sequences in database: 19,357\n",
" \n",
"Lambda K H\n",
" 1.37 0.711 1.31 \n",
"\n",
"Gapped\n",
"Lambda K H\n",
" 1.37 0.711 1.31 \n",
"\n",
"\n",
"Matrix: blastn matrix:1 -3\n",
"Gap Penalties: Existence: 5, Extension: 2\n",
"Number of Sequences: 19357\n",
"Number of Hits to DB: 1840\n",
"Number of extensions: 12\n",
"Number of successful extensions: 7\n",
"Number of sequences better than 10.0: 2\n",
"Number of HSP's gapped: 7\n",
"Number of HSP's successfully gapped: 2\n",
"Length of query: 71\n",
"Length of database: 3,678,086\n",
"Length adjustment: 14\n",
"Effective length of query: 57\n",
"Effective length of database: 3,407,088\n",
"Effective search space: 194204016\n",
"Effective search space used: 194204016\n",
"X1: 10 (19.8 bits)\n",
"X2: 15 (29.7 bits)\n",
"X3: 50 (99.1 bits)\n",
"S1: 10 (20.3 bits)\n",
"S2: 12 (24.3 bits)\n",
"\n",
"\n",
"\n"
]
}
],
"source": [
"p = BlastPDB(seq.seq)\n",
"p.search()\n",
"print p.result"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"scrolled": true
},
"outputs": [
{
"ename": "RfamSearchError",
"evalue": "Error: File existence/permissions problem in trying to open CM file /home/magnus/work/db/rfamdb/Rfam.cm.\nCM file /home/magnus/work/db/rfamdb/Rfam.cm not found (nor an .i1m binary of it); also looked in RFAMDB",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mRfamSearchError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;31m#seq = Seq.Seq(\"GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG\")\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mrs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mRfamSearch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0;32mprint\u001b[0m \u001b[0mrs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcmscan\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mseq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/Users/magnus/work-src/rna-pdb-tools/rna_pdb_tools/RfamSearch.pyc\u001b[0m in \u001b[0;36mcmscan\u001b[0;34m(self, seq)\u001b[0m\n\u001b[1;32m 62\u001b[0m \u001b[0merr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mo\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 63\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 64\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mRfamSearchError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 65\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutput\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mof\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 66\u001b[0m \u001b[0;31m# os.chdir(old_pwd)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mRfamSearchError\u001b[0m: Error: File existence/permissions problem in trying to open CM file /home/magnus/work/db/rfamdb/Rfam.cm.\nCM file /home/magnus/work/db/rfamdb/Rfam.cm not found (nor an .i1m binary of it); also looked in RFAMDB"
]
}
],
"source": [
"import rna_pdb_tools.RfamSearch as rf\n",
"#reload(rf)\n",
"\n",
"#seq = Seq.Seq(\"GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG\")\n",
"rs = rf.RfamSearch()\n",
"print rs.cmscan(seq)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# 3D structure analysis"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from rna_pdb_tools.pdb_parser_lib import RNAStructure\n",
"\n",
"fn = \"rna_pdb_tools/data/260c8ff6-f24e-4eff-9760-1831407fc770_ALL_thrs5.30A_clust01-000001_AA.pdb\"\n",
"\n",
"s = RNAStructure(fn)\n",
"print s.get_report()\n",
"print s.get_info_chains()\n",
"print s.get_head()\n",
"#print s.view() # image paste here :-)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"cd rna_pdb_tools\n",
"./rna-pdb-tools.py --no_hr --get_seq data/260c8ff6-f24e-4eff-9760-1831407fc770_ALL_thrs5.30A_clust01-000001_AA.pdb"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# RNA 3D structure prediction"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# model using SimRNA\n",
"#res = SimRNA(ss,seq.get_ss())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# fake import, should be \n",
"res = \"rna_pdb_tools/data/260c8ff6-f24e-4eff-9760-1831407fc770_ALL_thrs5.30A_clust01-000001_AA.pdb\"\n",
"# view\n",
"view = nglview.show_structure_file(res)\n",
"view.add_representation(repr_type='cartoon')\n",
"view"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# rna_pdb_tools --get_seq"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"cd ~/rna-bench/opt/xxxcx rna_pdb_tools\n",
"./rna-pdb-tools.py --no_hr --get_seq ~/rna-bench/examples/5k7c.pdb"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"cd rna_pdb_tools\n",
"./rna-pdb-tools.py --no_hr --get_seq input/5k7c.pdb\n",
"./rna-pdb-tools.py --no_hr --get_seq input/tetraloop.pdb\n",
"./rna-pdb-tools.py --get_seq input/1xjr.pdb"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
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"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
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"toc": {
"colors": {
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"moveMenuLeft": true,
"nav_menu": {
"height": "120px",
"width": "252px"
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"navigate_menu": true,
"number_sections": true,
"sideBar": true,
"threshold": 4,
"toc_cell": false,
"toc_section_display": "block",
"toc_window_display": false,
"widenNotebook": false
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"widgets": {
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