{ "metadata": { "name": "OlyO_Chi_Exp", "signature": "sha256:827b0f385a1e7ce4a6cc9efe03efab96d41f1779c9cef703f441ea600c3b97f4" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "#Influence of mechanical stress and photoperiod on _Ostrea lurida_\n", "Confirming molecular aspects of B. Chi's Capstone Project \n", "\n", "--\n", "\n", "##Primer Design\n", "\n", "" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!wget http://eagle.fish.washington.edu/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "--2013-07-12 07:55:37-- http://eagle.fish.washington.edu/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta\r\n", "Resolving eagle.fish.washington.edu... " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "128.95.149.81\r\n", "Connecting to eagle.fish.washington.edu|128.95.149.81|:80... connected.\r\n", "HTTP request sent, awaiting response... 200 OK\r\n", "Length: 26154986 (25M) [text/plain]\r\n", "Saving to: `Supp_1_Ostrea_lurida_transcriptome.fasta'\r\n", "\r\n", "\r", " 0% [ ] 0 --.-K/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "30% [==========> ] 7,872,512 36.9M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "54% [====================> ] 14,158,672 32.5M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "98% [=====================================> ] 25,867,368 40.1M/s \r", "100%[======================================>] 26,154,986 40.4M/s in 0.6s \r\n", "\r\n", "2013-07-12 07:55:38 (40.4 MB/s) - `Supp_1_Ostrea_lurida_transcriptome.fasta' saved [26154986/26154986]\r\n", "\r\n" ] } ], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">Ostrea_lur_contig1\r\n", "GATTTGACAGCCTCTATTTCTTGATTGGATTTGACAGCCTCTATTTCTTGGACCTGAAGTAGTCATTGAGAACATCCAGGGCTTGAGACTCCTTTCCGTAATCCTTGACTACCACACAGCTGCAGCCAACAACTTTCCTGGCTTTGCCCTCTTTGTCAATCTTACAAAGACCAGACCACTCTCCCAGTTTTTTGTTGTCATCAACCTTCAAAAGGTTGATCCCATGTTCAGCACAGAGTGCTTCCACCAGCTTTACATACATGGGTTCATCGCAGTTGTTGGCAAGAATGCACAAATGAGCTTGACGTTTGTCAAGGGCCTTTGCACACTCATGCAGTCCTTTTGCTAAACCATCGTGAATCATGGCCGTCTTCAGAACTTCCTGGACCGCTGTAAATACGTCCATCGATCCACCCGATACAGTGGGAACATCATCTCCTTCCGCATCCGACATTTTCGCGAAAACGGACGTCCTTAATGATGTTCCAAGAGAAGTT\r\n", ">Ostrea_lur_contig2\r\n", "ATATTGTCCGTTTTTGCGGCTGTCAGGTGTTTTGAAATGGAAGAAGACCAGATTCAGGTGGCCAACTTTGACGTGAAGCCAGGCGGCGCTCTGCTGTCGTTTGAGAAGGAATGGGACGAAATCACCTGCAGATTTTCATATCGGGCACAGGGTGGAACCAATGAGCTGTGGAATCTGGGAATGGTGCAGAGTAAAGATGGCCGCGATTTCAGCTGCTCTGTAGAACGTCCGAGCGGCCAGTCCTACCTCTTCTTCCAGGCCTTTAAACTGGAAGTGACCGGAATCCCAACTGTAGAAGGGGAAGTCTATGGACCTGGAATGACTCCACTGAAGTCCGAGGAATTCGAATTCGACAAGGCCGCTAATCAAATTACAGAGACCGGGAAGTTCCACTCTCAGCTGGACAAAGTTGTGCTCTATGCCCGAAGGGGAAAATCCGAGTTATAATCCAGCCAAGAATCGAACCATCCAAACTCCTAACAGTTGGCAGTCTACAAAGAGTTCAAATGTTCCAAATTTTGATGACATGTTATTGACACATGTTTTATCTTTGTACTAAAAATGGGGGGATTTTATTGATGATGAAGCAAAATGGCAGCATCAATTTACAAGAGTTTTTCTCATTGAAAAGAATGTAGACTGTAATAGATTTAAAATAGTGTTATCTAAATCAAATTGATGGGAATTATCAGAAGGTGTAAAGTAGAATTGAATGTAGATTTCCTGTGTTGTATACCTTAGGTGTTCAATAGGCTCTGTATTGTAATCGGCATTATAAAAAAAAATCTGGGCCACTACTGTACACAGGGAAATAATTTTCACCTTTGTTATGGGAGGCCAAGATAGGGGAAACTTTTAACCAGAGTTACCTCTCTTTTGACACAACATAAAAATGGGTTGTACCTGTTTACACGTGTAGAAAAGTGAAAATTAAAATAGGTCCAAAACATCCCGTGTGTACAGGTGGTTTAGGTTAAACAGGAAATTAGACTTTCTGTTAATTAATCGCTTTACGGAGGGTAGTAGCTGGAGATTTTTATTTACAGCAACATAAAATGTCAAGTCACATTCAAGCGTCTCGTCTGATGATTGTTCTGTAGCGATTGGGTGTTTGTATGTAATCTATCCTGTAAGGATATTGTATGTAATCTATCCTGTAA\r\n", ">Ostrea_lur_contig3\r\n", "CCCTCTGTCTGTCCTTCCATGCACGCAGGGGGCCCTTGTTAGGTTTATATTGTACGGTAACTCCATCAGGGATCAGGCGCCCGTCCGCTCTCATCACCTCGTACTGAGGCTTCTCCCACTTAGTGAATCCCCACTTCTTGGACACGTGGATCTTCTGACGTCCGGGGAACTTGAACTTGGCTCTCCTGAGTGCTTCTATCACGGCAGCCTGGTGACTCTCACGAGCACGTACAGACATGATTGGCTGTCCTATGTGTACACGGGCTACGGTGCCTTGTGGTTTACCAAAAGCTCCTCTCATTCCCGTCTGAAGCCTATCGGCTCCAGCGCACGACAACATCTTGTTGATTCTGATGACGTGGAAGGGGTGCACTCGAATTCGCATGTGGAAAGCATCTTTACCACAGTTCTTGACCAAATACTTGTTGGCACAGATACGTCCTGCTTCTAGAGCTTCCGAGGAGAGCTGTTCGTACTCATCAGATACGAGATGCACACACAGGGGGAAGTCATCTACCTTGGCCTTCTTCCTCCCAAGATCAAAAATACGGATCTTTGCATCTGGGACACCTCTACAAAATCTGGACTTCGGATAAGGTTTGTTCTTACAGTACCGGTAACACCGAGCTGGTCGGCGTCCCATTTTGAATTAGAA\r\n", ">Ostrea_lur_contig4\r\n", "CAAAAATATAAGACAAGCGTAATTAAAACCTACTTTTAAAAATGTACATGCTTTATCTACGATAAGCAATAACTTTTAAGCTACATGTATGATACACATTGTTTAGCAGTTACGATTGCATGTATCTCACTATATCTTTTCTCTATTAGCGCCTTACAGATACTCGTCCCGCTTTCGGTTCATCGGTACTTCTTCCTCCAAATTGTCACTTATTGTCTTGTCTTTGGTTTCCTTCAGCAAAAGGCACGTAATTGCAGAGGCCAACATCACAATAAAACATATTATGTACATTACTCCTGGGTTCTCTTTGTTCACAACAACGAGTTGAGGCGCTATCAAAGCTCCTATACGAGAGATCGAGTTTTGGGTTCCATAACCGATGTTCCTGACGACAGTTGGATACACTTCCGTTGTGAAGGCTATGATGGCAGCCCAAGACGCAGAGACACCAAACTTGGCTGCCAG\r\n", ">Ostrea_lur_contig5\r\n", "CAGCCCAAGTCGAGTGCATTTGGACGATGGAACATATTGGTCAGAAAGAGCAGCGTTATTTCAAGGAAAATCTCATCGACAAGTGTTTAACGACAGCATGAGCAAGCTCTACTCCAAAATGTACCGGAACGCGCTGCGTCCAGGGCCGATCTGATAGTTTATACCTCAGTAGATTCCTCTCAGCTGTGATATTAGATAGTGTCTGTGTATATTTATGATATTTAGGATAAAAGCTATGTGACTCCAGCCATTTCCTGGCACTAAAAGTTTCACTTCAAAACATATGTTGTCTACCATTTTGTCTATTTTTTTATGTTACTAGTGCTCTGTTAACTTTTGATCAGTGAAATTGTTGGTGGCTTTTGATTTGGGGTCTCGGATTCCGTAACTTTTATCCGTGCTTGTTTTGTGTGACAGTACTCGAGTAGTGTGGCCAGTGACACAGAGTTTGTATGGGGGAGGCGGAGTTATCTCTTGCAGGTATCCCAGGGTTCCTCTTACAGGTATCCCAGGATTCCACCTGGTTACCAAACGTCTGACAAATGAAATAAAGCGTATCTTTTGTTTTTGACTGGGTGTAGAGAATCAAAATGTATAATTGCTCCAATATTACAGGGATGTGTATAGCTTTTCAGATTTTAATATAACAATTCCTATTTCCATAAATGTCTCATTTTAGTGTTTTTTTTATTTTATATAATATGCAGCACAAGCCTACACATGATTATATTAATACGGAATCAGCTGGCTTTTATTGTATCACA\r\n" ] } ], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">Ostrea_lur_contig41132\r\n", "AAATTTATAGGAATCCCCCGTCCACCCACAACTGAGAAAACAGACTTGTTCGATATTGATTTATCACAATGACCGCAACCTTGAAGTGTGAAGTTTCAGATCATGTAGTACAAATCAAAGAAAAAATAGAAATACAAATGCTTGCAAAATGATTTAGATAATCTACCTATTATCTGAGATATATTTGTGGTAAACTAAGTAGTTCATATTTGATATTTTTGGTAAAAATTCAATTTTATTTCTCTGTTTATTTATTTTATTTTTAAAAGTTAGGATGTATTTTCAATACAGTTT\r\n", ">Ostrea_lur_contig41133\r\n", "GGCTAATACAATATTGGAATCAGTAAACACCTGTACACAAAGTTTAGTGAAAATATGAAATGGCATGTGTCGGCCTTTGTCTGATTATACACTGGACAGCCTCTTTTTTTAAAATGTTTTTAAAATCATTGGTTCTATTGGGAATTTTACAAGGTCGTTTAGAACATAGACGATTTAGTGCCGATAGAAAAGCACTATAAATGTGCACTGGAGAACACGTCTACAATAAGG\r\n", ">Ostrea_lur_contig41134\r\n", "ATATGAAAAAACAGACAGTCAATAAGGAAGCTCAATTTGTGCCCATGGGAATTCTAAGATCATGACATCAGTTAATGGCCTTATAATTAACAACAAGGCTACATGTACCCCGTTCAAATGGAAAGTAAACAGATATTAGAGACGGAGCGCTTCAACAGTACTATGTTTTACAGCAAGTTTCATAGAAATGTATATTGTCAGTTTTGATGACGTCATGCATCTTGTCAATTACCTTTACTGCTTCGTCTTTTCC\r\n", ">Ostrea_lur_contig41135\r\n", "GGTAGATCTATCTAATGTTTGGGCTATCAGCTGGCTATCAATGCAATGATGTTCAGTTCTCTAATAATCACGGAGATAGTTTGTGGAAAAGATAGATTATTCATTCTACGGAAGTTGAAATAGATTGATCTATTCATTTCTAAATGTAATCAGGTGATTAGAGGTTTAGTTATACTGATTTAATGTATTCCTGTCAAACAGGTACCCGATGGCTACCTATCA\r\n", ">Ostrea_lur_contig41136\r\n", "TTTATAAACCTGTAAAATAAGTTTATTCACCAATCGTGGACCCTTTACATGCAATCGTCTAAAACCATTGCCGTTCAATATAGGTATCATCTAGATTTGAAAGTTTGATTTCAGTATTACCGATTTAGCATGGATTATACTGATCTCAAACCGGCCACGATTGTTCTATGGTGACGTCTCCATATGAGTGAAATATTCTCGAGTGGGACGTAAAACAATAA\r\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Users/sr320/Desktop/0001_DataS1.fa" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">Ostrea_lur_contig41132\r\n", "AAATTTATAGGAATCCCCCGTCCACCCACAACTGAGAAAACAGACTTGTTCGATATTGATTTATCACAATGACCGCAACCTTGAAGTGTGAAGTTTCAGATCATGTAGTACAAATCAAAGAAAAAATAGAAATACAAATGCTTGCAAAATGATTTAGATAATCTACCTATTATCTGAGATATATTTGTGGTAAACTAAGTAGTTCATATTTGATATTTTTGGTAAAAATTCAATTTTATTTCTCTGTTTATTTATTTTATTTTTAAAAGTTAGGATGTATTTTCAATACAGTTT\r\n", ">Ostrea_lur_contig41133\r\n", "GGCTAATACAATATTGGAATCAGTAAACACCTGTACACAAAGTTTAGTGAAAATATGAAATGGCATGTGTCGGCCTTTGTCTGATTATACACTGGACAGCCTCTTTTTTTAAAATGTTTTTAAAATCATTGGTTCTATTGGGAATTTTACAAGGTCGTTTAGAACATAGACGATTTAGTGCCGATAGAAAAGCACTATAAATGTGCACTGGAGAACACGTCTACAATAAGG\r\n", ">Ostrea_lur_contig41134\r\n", "ATATGAAAAAACAGACAGTCAATAAGGAAGCTCAATTTGTGCCCATGGGAATTCTAAGATCATGACATCAGTTAATGGCCTTATAATTAACAACAAGGCTACATGTACCCCGTTCAAATGGAAAGTAAACAGATATTAGAGACGGAGCGCTTCAACAGTACTATGTTTTACAGCAAGTTTCATAGAAATGTATATTGTCAGTTTTGATGACGTCATGCATCTTGTCAATTACCTTTACTGCTTCGTCTTTTCC\r\n", ">Ostrea_lur_contig41135\r\n", "GGTAGATCTATCTAATGTTTGGGCTATCAGCTGGCTATCAATGCAATGATGTTCAGTTCTCTAATAATCACGGAGATAGTTTGTGGAAAAGATAGATTATTCATTCTACGGAAGTTGAAATAGATTGATCTATTCATTTCTAAATGTAATCAGGTGATTAGAGGTTTAGTTATACTGATTTAATGTATTCCTGTCAAACAGGTACCCGATGGCTACCTATCA\r\n", ">Ostrea_lur_contig41136\r\n", "TTTATAAACCTGTAAAATAAGTTTATTCACCAATCGTGGACCCTTTACATGCAATCGTCTAAAACCATTGCCGTTCAATATAGGTATCATCTAGATTTGAAAGTTTGATTTCAGTATTACCGATTTAGCATGGATTATACTGATCTCAAACCGGCCACGATTGTTCTATGGTGACGTCTCCATATGAGTGAAATATTCTCGAGTGGGACGTAAAACAATAA\r\n" ] } ], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": [ "#confirmed file in question was published on Figshare and MER Notes. " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 19 }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "code", "collapsed": false, "input": [ "#not looking good re the word doc and the data.\n", "#will try to blast primers as independant verification" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "!makeblastdb -in /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\\+/db/OlyO_transcriptome_v1" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "\r\n", "Building a new DB, current time: 07/12/2013 08:23:28\r\n", "New DB name: /Volumes/Bay3/Software/ncbi-blast-2.2.27+/db/OlyO_transcriptome_v1\r\n", "New DB title: /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta\r\n", "Sequence type: Nucleotide\r\n", "Keep Linkouts: T\r\n", "Keep MBits: T\r\n", "Maximum file size: 1000000000B\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Adding sequences from FASTA; added 41136 sequences in 2.70528 seconds.\r\n" ] } ], "prompt_number": 39 }, { "cell_type": "code", "collapsed": false, "input": [ "#query sequence needs to be primers" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 40 }, { "cell_type": "code", "collapsed": false, "input": [ "!blastn -query /Volumes/web/cnidarian/OlyO_Chi_primers.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\\+/db/OlyO_transcriptome_v1 -out /Volumes/web/cnidarian/OlyO_Chi_primers_blastn1 -word_size 20 -outfmt 6 " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 48 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/OlyO_Chi_primers_blastn1" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "BagF\tOstrea_lur_contig28411\t100.00\t20\t0\t0\t1\t20\t308\t327\t3e-04\t38.1\r\n", "BagR\tOstrea_lur_contig28411\t100.00\t22\t0\t0\t1\t22\t408\t387\t3e-05\t41.7\r\n", "HspF\tOstrea_lur_contig402\t100.00\t20\t0\t0\t1\t20\t1879\t1898\t3e-04\t38.1\r\n", "HspR\tOstrea_lur_contig402\t100.00\t20\t0\t0\t1\t20\t2027\t2008\t3e-04\t38.1\r\n", "U2aF\tOstrea_lur_contig2667\t100.00\t20\t0\t0\t1\t20\t638\t657\t3e-04\t38.1\r\n", "U2aR\tOstrea_lur_contig2667\t100.00\t20\t0\t0\t1\t20\t767\t748\t3e-04\t38.1\r\n", "PygmF\tOstrea_lur_contig95\t100.00\t20\t0\t0\t1\t20\t912\t931\t3e-04\t38.1\r\n", "PygmR\tOstrea_lur_contig95\t100.00\t20\t0\t0\t1\t20\t1042\t1023\t3e-04\t38.1\r\n", "IgfrF\tOstrea_lur_contig16177\t100.00\t20\t0\t0\t1\t20\t1997\t2016\t3e-04\t38.1\r\n", "IgfrR\tOstrea_lur_contig16177\t100.00\t20\t0\t0\t1\t20\t2097\t2078\t3e-04\t38.1\r\n" ] } ], "prompt_number": 49 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"Ostrea_lur_contig28411\" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Ostrea_lur_contig28411\tQ3ZBG5\t9.00E-21\tBAG2_BOVIN BAG family molecular chaperone regulator 2 OS=Bos taurus PE=2 SV=1\r\n" ] } ], "prompt_number": 68 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -w \"Ostrea_lur_contig402\" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt\n", "#need exact mactch to exclude 402X -w" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Ostrea_lur_contig402\tQ9GKX8\t0\tHS90B_HORSE Heat shock protein HSP 90-beta OS=Equus caballus GN=HSP90AB1 PE=2 SV=3\r\n" ] } ], "prompt_number": 73 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -w \"Ostrea_lur_contig2667\" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Ostrea_lur_contig2667\tQ3T127\t3.00E-104\tU2AF4_BOVIN Splicing factor U2AF 26 kDa subunit OS=Bos taurus GN=U2AF1L4 PE=2 SV=1\r\n" ] } ], "prompt_number": 74 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -w \"Ostrea_lur_contig95\" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Ostrea_lur_contig95\tQ9WUB3\t0\t\"PYGM_MOUSE Glycogen phosphorylase, muscle form OS=Mus musculus GN=Pygm PE=1 SV=3\"\r\n" ] } ], "prompt_number": 75 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -w \"Ostrea_lur_contig16177\" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Ostrea_lur_contig16177\tQ05688\t1.00E-138\tIGF1R_BOVIN Insulin-like growth factor 1 receptor (Fragment) OS=Bos taurus GN=IGF1R PE=2 SV=1\r\n" ] } ], "prompt_number": 76 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }