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Minor changes to the BLAST notebook
This includes changing the font size in the BLAST flashcard so that the text is legible.
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Lines changed: 205 additions & 26 deletions

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‎html/flashcard_blastout.html‎

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}
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.back .flashcardtext{
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font-size: 0.2em;
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font-size: 1.2em;
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}
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‎module_notebooks/03-searching-graphs-with-blast.ipynb‎

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"source": [
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"\n",
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"## Overview\n",
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"Here you will learn how to search graphs with BLAST. In other words, you can use a DNA sequence, such as your favorite gene, to search the pangenomic graph, discover the structure of the graph, and explore homologous sequences."
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"In this submodule you will learn how to search graphs with BLAST. In other words, you can use a DNA sequence, such as your favorite gene, to search the pangenomic graph, discover the structure of the graph, and explore homologous sequences."
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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">S288C_chrVIII:213043-213228/rc\n",
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"ATGTTCAGCGAATTAATTAACTTCCAAAATGAAGGTCATGAGTGCCAATG\n",
107+
"CCAATGTGGTAGCTGCAAAAATAATGAACAATGCCAAAAATCATGTAGCT\n",
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"GCCCAACGGGGTGTAACAGCGACGACAAATGCCCCTGCGGTAACAAGTCT\n",
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"GAAGAAACCAAGAAGTCATGCTGCTCTGGGAAATGA\n",
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">S288C_chrVIII:213693-214757/rc\n",
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"ATGGTACCCGCTGCTGAAAACCTATCTCCGATACCTGCCTCTATTGATAC\n",
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"GAACGACATTCCTTTAATTGCTAACGATTTAAAATTACTGGAAACGCAAG\n",
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"CAAAATTGATAAATATTCTGCAAGGTGTTCCTTTCTACTTGCCAGTAAAT\n",
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"TTAACCAAAATTGAAAGTCTGTTAGAAACCTTGACTATGGGCGTGAGTAA\n",
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"TACAGTAGACTTATATTTTCATGACAACGAAGTCAGAAAAGAATGGAAAG\n",
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"ACACTTTAAATTTTATCAATACCATTGTTTATACAAATTTTTTCCTTTTT\n",
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"GTTCAAAACGAATCCTCTTTGTCCATGGCAGTTCAACATTCTTCTAACAA\n",
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"CAATAAGACCTCGAACTCTGAAAGATGTGCAAAGGATCTGATGAAAATTA\n",
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"TTTCTAATATGCACATTTTTTACTCAATAACATTTAATTTTATCTTCCCC\n",
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"ATAAAGTCGATAAAGTCATTTTCAAGCGGCAATAATCGCTTTCATTCTAA\n",
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"TGGTAAAGAATTTTTATTCGCAAATCATTTTATTGAAATCTTACAGAATT\n",
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"TTATAGCAATCACATTTGCTATTTTCCAACGTTGTGAAGTAATATTATAT\n",
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"GACGAATTTTACAAAAATCTTTCAAATGAGGAGATTAATGTTCAATTGCT\n",
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"ATTGATTCATGACAAGATTTTGGAAATTTTAAAAAAAATAGAAATTATCG\n",
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"TATCCTTTTTACGAGATGAAATGAATAGCAACGGAAGTTTCAAATCTATT\n",
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"AAAGGTTTCAACAAGGTTTTGAATCTGATTAAATATATGCTGAGATTTAG\n",
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"CAAGAAAAAACAAAATTTTGCGAGAAACTCTGATAACAATAATGTTACAG\n",
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"ATTATAGTCAGTCGGCGAAGAACAAAAATGTTCTCTTGAAATTCCCCGTT\n",
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"AGTGAACTGAACAGAATCTATTTAAAATTTAAGGAGATTTCAGATTTTTT\n",
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"AATGGAAAGAGAAGTTGTCCAAAGGAGTATAATTATTGACAAGGATTTGG\n",
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"AATCTGATAATCTGGGTATTACTACGGCAAACTTCAACGATTTCTATGAT\n",
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"GCATTTTATAATTAG\n"
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]
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}
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],
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"source": [
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"!cat genes/genes.fa"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 4,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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">CUP1\n",
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"ATGTTCAGCGAATTAATTAACTTCCAAAATGAAGGTCATGAGTGCCAATG\n",
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"CCAATGTGGTAGCTGCAAAAATAATGAACAATGCCAAAAATCATGTAGCT\n",
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"GCCCAACGGGGTGTAACAGCGACGACAAATGCCCCTGCGGTAACAAGTCT\n",
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"GAAGAAACCAAGAAGTCATGCTGCTCTGGGAAATGA\n",
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">YHR054C\n",
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"ATGGTACCCGCTGCTGAAAACCTATCTCCGATACCTGCCTCTATTGATAC\n",
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"GAACGACATTCCTTTAATTGCTAACGATTTAAAATTACTGGAAACGCAAG\n",
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"CAAAATTGATAAATATTCTGCAAGGTGTTCCTTTCTACTTGCCAGTAAAT\n",
187+
"TTAACCAAAATTGAAAGTCTGTTAGAAACCTTGACTATGGGCGTGAGTAA\n",
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"TACAGTAGACTTATATTTTCATGACAACGAAGTCAGAAAAGAATGGAAAG\n",
189+
"ACACTTTAAATTTTATCAATACCATTGTTTATACAAATTTTTTCCTTTTT\n",
190+
"GTTCAAAACGAATCCTCTTTGTCCATGGCAGTTCAACATTCTTCTAACAA\n",
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"CAATAAGACCTCGAACTCTGAAAGATGTGCAAAGGATCTGATGAAAATTA\n",
192+
"TTTCTAATATGCACATTTTTTACTCAATAACATTTAATTTTATCTTCCCC\n",
193+
"ATAAAGTCGATAAAGTCATTTTCAAGCGGCAATAATCGCTTTCATTCTAA\n",
194+
"TGGTAAAGAATTTTTATTCGCAAATCATTTTATTGAAATCTTACAGAATT\n",
195+
"TTATAGCAATCACATTTGCTATTTTCCAACGTTGTGAAGTAATATTATAT\n",
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"GACGAATTTTACAAAAATCTTTCAAATGAGGAGATTAATGTTCAATTGCT\n",
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"ATTGATTCATGACAAGATTTTGGAAATTTTAAAAAAAATAGAAATTATCG\n",
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"TATCCTTTTTACGAGATGAAATGAATAGCAACGGAAGTTTCAAATCTATT\n",
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"AAAGGTTTCAACAAGGTTTTGAATCTGATTAAATATATGCTGAGATTTAG\n",
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"CAAGAAAAAACAAAATTTTGCGAGAAACTCTGATAACAATAATGTTACAG\n",
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"ATTATAGTCAGTCGGCGAAGAACAAAAATGTTCTCTTGAAATTCCCCGTT\n",
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"AGTGAACTGAACAGAATCTATTTAAAATTTAAGGAGATTTCAGATTTTTT\n",
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"AATGGAAAGAGAAGTTGTCCAAAGGAGTATAATTATTGACAAGGATTTGG\n",
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"AATCTGATAATCTGGGTATTACTACGGCAAACTTCAACGATTTCTATGAT\n",
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"GCATTTTATAATTAG\n"
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]
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}
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],
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"source": [
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"!cat genes/genes.fa"
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"\n",
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"## BLAST\n",
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"\n",
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"The Basic Local Alignment Search Tool (BLAST) tool allows you to compare DNA sequences in order to efficiently identify the best matches. Here we will use BLAST to search the DNA sequences in the pangenome for matches to two adjacent genes.\n",
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"\n",
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"Altschul, Stephen F., et al. \"Basic local alignment search tool.\" Journal of molecular biology 215.3 (1990): 403-410.\n",
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"The Basic Local Alignment Search Tool (BLAST) tool allows you to compare DNA sequences in order to efficiently identify the best matches. Here we will use BLAST to search the DNA sequences in the pangenome for matches to two adjacent genes ([Altschul, Stephen F., et al. 1990](https://doi.org/10.1016/S0022-2836(05)80360-2)).\n",
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"\n",
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"\n",
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"### BLAST the graph manually\n",
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{
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"metadata": {},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"[M::main] Version: 0.4-r214-dirty\n",
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"[M::main] CMD: gfatools gfa2fa graphs/yprp.chrVIII.pggb.gfa\n",
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"[M::main] Real time: 0.020 sec; CPU: 0.021 sec\n"
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]
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}
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],
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"source": [
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"!gfatools gfa2fa graphs/yprp.chrVIII.pggb.gfa > graphs/yprp.chrVIII.pggb.fa"
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},
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{
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n",
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"\n",
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"Building a new DB, current time: 04/28/2025 21:33:30\n",
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"New DB name: /home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/graphs/yprp.chrVIII.pggb.fa\n",
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"New DB title: graphs/yprp.chrVIII.pggb.fa\n",
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"Sequence type: Nucleotide\n",
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"Keep MBits: T\n",
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"Maximum file size: 3000000000B\n",
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"Adding sequences from FASTA; added 19252 sequences in 0.19645 seconds.\n",
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"\n",
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"\n"
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]
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}
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],
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"source": [
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"!makeblastdb -in graphs/yprp.chrVIII.pggb.fa -input_type fasta -dbtype nucl"
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"CUP1\t7899\t100.000\t186\t0\t0\t1\t186\t456\t271\t9.20e-97\t344\n",
356+
"CUP1\t7715\t100.000\t186\t0\t0\t1\t186\t1524\t1339\t9.20e-97\t344\n",
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"CUP1\t7715\t100.000\t186\t0\t0\t1\t186\t5523\t5338\t9.20e-97\t344\n",
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"CUP1\t7715\t100.000\t186\t0\t0\t1\t186\t7521\t7336\t9.20e-97\t344\n",
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"CUP1\t7715\t99.462\t186\t0\t1\t1\t186\t3521\t3337\t1.54e-94\t337\n",
360+
"CUP1\t7773\t99.457\t184\t1\t0\t1\t184\t1130\t947\t5.54e-94\t335\n",
361+
"CUP1\t7851\t100.000\t164\t0\t0\t1\t164\t164\t1\t1.56e-84\t303\n",
362+
"CUP1\t7790\t100.000\t164\t0\t0\t1\t164\t164\t1\t1.56e-84\t303\n",
363+
"CUP1\t7732\t100.000\t164\t0\t0\t1\t164\t164\t1\t1.56e-84\t303\n",
364+
"CUP1\t7698\t100.000\t164\t0\t0\t1\t164\t164\t1\t1.56e-84\t303\n",
365+
"CUP1\t7638\t100.000\t164\t0\t0\t1\t164\t164\t1\t1.56e-84\t303\n",
366+
"CUP1\t7602\t100.000\t134\t0\t0\t31\t164\t134\t1\t7.42e-68\t248\n",
367+
"CUP1\t7605\t100.000\t29\t0\t0\t1\t29\t29\t1\t1.74e-09\t54.7\n",
368+
"YHR054C\t7715\t100.000\t1065\t0\t0\t1\t1065\t3053\t1989\t0.0\t1967\n",
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"YHR054C\t7715\t100.000\t1065\t0\t0\t1\t1065\t7052\t5988\t0.0\t1967\n",
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"YHR054C\t7715\t100.000\t1065\t0\t0\t1\t1065\t9050\t7986\t0.0\t1967\n",
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"YHR054C\t7715\t99.626\t1069\t0\t4\t1\t1065\t5054\t3986\t0.0\t1949\n",
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"YHR054C\t7715\t100.000\t1054\t0\t0\t1\t1054\t1054\t1\t0.0\t1947\n",
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"YHR054C\t7899\t99.905\t1053\t1\t0\t13\t1065\t1973\t921\t0.0\t1940\n",
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"YHR054C\t7883\t100.000\t286\t0\t0\t428\t713\t286\t1\t1.27e-151\t529\n",
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"YHR054C\t7821\t100.000\t286\t0\t0\t428\t713\t286\t1\t1.27e-151\t529\n",
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"YHR054C\t7763\t100.000\t286\t0\t0\t428\t713\t286\t1\t1.27e-151\t529\n",
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"YHR054C\t7671\t100.000\t261\t0\t0\t428\t688\t261\t1\t1.01e-137\t483\n",
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"YHR054C\t7892\t100.000\t210\t0\t0\t126\t335\t210\t1\t2.26e-109\t388\n",
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"YHR054C\t7827\t100.000\t210\t0\t0\t126\t335\t210\t1\t2.26e-109\t388\n",
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"YHR054C\t7769\t100.000\t210\t0\t0\t126\t335\t210\t1\t2.26e-109\t388\n",
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"YHR054C\t7677\t100.000\t210\t0\t0\t126\t335\t210\t1\t2.26e-109\t388\n",
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"YHR054C\t7874\t100.000\t129\t0\t0\t838\t966\t129\t1\t2.40e-64\t239\n",
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"YHR054C\t7812\t100.000\t129\t0\t0\t838\t966\t129\t1\t2.40e-64\t239\n",
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"YHR054C\t7754\t100.000\t129\t0\t0\t838\t966\t129\t1\t2.40e-64\t239\n",
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"YHR054C\t7660\t100.000\t129\t0\t0\t838\t966\t129\t1\t2.40e-64\t239\n",
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"YHR054C\t7895\t100.000\t111\t0\t0\t14\t124\t111\t1\t2.44e-54\t206\n",
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"YHR054C\t7830\t100.000\t111\t0\t0\t14\t124\t111\t1\t2.44e-54\t206\n",
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"YHR054C\t7772\t100.000\t111\t0\t0\t14\t124\t111\t1\t2.44e-54\t206\n",
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"YHR054C\t7680\t100.000\t111\t0\t0\t14\t124\t111\t1\t2.44e-54\t206\n",
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"YHR054C\t7877\t100.000\t99\t0\t0\t738\t836\t99\t1\t1.14e-47\t183\n",
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"YHR054C\t7815\t100.000\t99\t0\t0\t738\t836\t99\t1\t1.14e-47\t183\n",
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"YHR054C\t7757\t100.000\t99\t0\t0\t738\t836\t99\t1\t1.14e-47\t183\n",
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"YHR054C\t7663\t100.000\t99\t0\t0\t738\t836\t99\t1\t1.14e-47\t183\n",
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"YHR054C\t7809\t100.000\t98\t0\t0\t968\t1065\t108\t11\t4.11e-47\t182\n",
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"YHR054C\t7751\t100.000\t98\t0\t0\t968\t1065\t108\t11\t4.11e-47\t182\n",
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"YHR054C\t7657\t100.000\t98\t0\t0\t968\t1065\t108\t11\t4.11e-47\t182\n",
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"YHR054C\t7824\t100.000\t90\t0\t0\t337\t426\t90\t1\t1.15e-42\t167\n",
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"YHR054C\t7766\t100.000\t90\t0\t0\t337\t426\t90\t1\t1.15e-42\t167\n",
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"YHR054C\t7674\t100.000\t90\t0\t0\t337\t426\t90\t1\t1.15e-42\t167\n",
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"YHR054C\t7871\t100.000\t87\t0\t0\t968\t1054\t87\t1\t5.35e-41\t161\n",
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"YHR054C\t7886\t100.000\t75\t0\t0\t352\t426\t75\t1\t2.51e-34\t139\n"
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]
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}
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],
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"source": [
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"!cat genes/genesXyprp.chrVIII.pggb.fa.txt"
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"cell_type": "code",
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"execution_count": 12,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/html": [
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"\n",
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" <iframe\n",
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" width=\"800\"\n",
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" height=\"400\"\n",
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" src=\"../html/flashcard_blastout.html\"\n",
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" frameborder=\"0\"\n",
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" allowfullscreen\n",
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" \n",
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" ></iframe>\n",
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" "
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],
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"text/plain": [
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"<IPython.lib.display.IFrame at 0x7f1ac5ddcf80>"
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]
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},
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"execution_count": 12,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"from IPython.display import IFrame\n",
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"IFrame('../html/blastout.html', width=800, height=400)"
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"IFrame('../html/flashcard_blastout.html', width=800, height=400)"
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},
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{
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"\n",
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"## Conclusion\n",
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"\n",
312-
"You learned how to blast against a pangenomic graph. Specifically, you searched for the CUP1 and YHR054C genes in the graph.\n",
485+
"In this submodule, you learned how to BLAST against a pangenomic graph. Specifically, you searched for the CUP1 and YHR054C genes in the graph.\n",
313486
"\n",
314-
"BLASTing gene sequences allows you to find out where genes of interest are in the fasta file exported from the pangenomic graph. It also allows you to identify copy numbers of the genes.\n",
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"BLASTing gene sequences allows you to find out where genes of interest are in the FASTA file exported from the pangenomic graph. It also allows you to identify copy numbers of the genes.\n",
315488
"\n",
316-
"In the next chapter you will learn how visualize graphs and to blast directly against the graph and visualize the result.\n",
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"In the next submodule you will learn how visualize graphs and to BLAST directly against the graph and visualize the result.\n",
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"\n",
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"----------------------"
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]
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}
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],
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"metadata": {
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"environment": {
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"kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
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"name": "workbench-notebooks.m129",
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"type": "gcloud",
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"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
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},
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"kernelspec": {
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"display_name": "nigms-pangenomics",
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"display_name": "nigms-pangenomics (Local)",
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"language": "python",
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"name": "conda-env-nigms-pangenomics-nigms-pangenomics"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.9"
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"version": "3.12.10"
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}
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},
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"nbformat": 4,

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