!wget http://eagle.fish.washington.edu/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta
--2013-07-12 07:55:37-- http://eagle.fish.washington.edu/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta Resolving eagle.fish.washington.edu... 128.95.149.81 Connecting to eagle.fish.washington.edu|128.95.149.81|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 26154986 (25M) [text/plain] Saving to: `Supp_1_Ostrea_lurida_transcriptome.fasta' 100%[======================================>] 26,154,986 40.4M/s in 0.6s 2013-07-12 07:55:38 (40.4 MB/s) - `Supp_1_Ostrea_lurida_transcriptome.fasta' saved [26154986/26154986]
!head /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta
>Ostrea_lur_contig1 GATTTGACAGCCTCTATTTCTTGATTGGATTTGACAGCCTCTATTTCTTGGACCTGAAGTAGTCATTGAGAACATCCAGGGCTTGAGACTCCTTTCCGTAATCCTTGACTACCACACAGCTGCAGCCAACAACTTTCCTGGCTTTGCCCTCTTTGTCAATCTTACAAAGACCAGACCACTCTCCCAGTTTTTTGTTGTCATCAACCTTCAAAAGGTTGATCCCATGTTCAGCACAGAGTGCTTCCACCAGCTTTACATACATGGGTTCATCGCAGTTGTTGGCAAGAATGCACAAATGAGCTTGACGTTTGTCAAGGGCCTTTGCACACTCATGCAGTCCTTTTGCTAAACCATCGTGAATCATGGCCGTCTTCAGAACTTCCTGGACCGCTGTAAATACGTCCATCGATCCACCCGATACAGTGGGAACATCATCTCCTTCCGCATCCGACATTTTCGCGAAAACGGACGTCCTTAATGATGTTCCAAGAGAAGTT >Ostrea_lur_contig2 ATATTGTCCGTTTTTGCGGCTGTCAGGTGTTTTGAAATGGAAGAAGACCAGATTCAGGTGGCCAACTTTGACGTGAAGCCAGGCGGCGCTCTGCTGTCGTTTGAGAAGGAATGGGACGAAATCACCTGCAGATTTTCATATCGGGCACAGGGTGGAACCAATGAGCTGTGGAATCTGGGAATGGTGCAGAGTAAAGATGGCCGCGATTTCAGCTGCTCTGTAGAACGTCCGAGCGGCCAGTCCTACCTCTTCTTCCAGGCCTTTAAACTGGAAGTGACCGGAATCCCAACTGTAGAAGGGGAAGTCTATGGACCTGGAATGACTCCACTGAAGTCCGAGGAATTCGAATTCGACAAGGCCGCTAATCAAATTACAGAGACCGGGAAGTTCCACTCTCAGCTGGACAAAGTTGTGCTCTATGCCCGAAGGGGAAAATCCGAGTTATAATCCAGCCAAGAATCGAACCATCCAAACTCCTAACAGTTGGCAGTCTACAAAGAGTTCAAATGTTCCAAATTTTGATGACATGTTATTGACACATGTTTTATCTTTGTACTAAAAATGGGGGGATTTTATTGATGATGAAGCAAAATGGCAGCATCAATTTACAAGAGTTTTTCTCATTGAAAAGAATGTAGACTGTAATAGATTTAAAATAGTGTTATCTAAATCAAATTGATGGGAATTATCAGAAGGTGTAAAGTAGAATTGAATGTAGATTTCCTGTGTTGTATACCTTAGGTGTTCAATAGGCTCTGTATTGTAATCGGCATTATAAAAAAAAATCTGGGCCACTACTGTACACAGGGAAATAATTTTCACCTTTGTTATGGGAGGCCAAGATAGGGGAAACTTTTAACCAGAGTTACCTCTCTTTTGACACAACATAAAAATGGGTTGTACCTGTTTACACGTGTAGAAAAGTGAAAATTAAAATAGGTCCAAAACATCCCGTGTGTACAGGTGGTTTAGGTTAAACAGGAAATTAGACTTTCTGTTAATTAATCGCTTTACGGAGGGTAGTAGCTGGAGATTTTTATTTACAGCAACATAAAATGTCAAGTCACATTCAAGCGTCTCGTCTGATGATTGTTCTGTAGCGATTGGGTGTTTGTATGTAATCTATCCTGTAAGGATATTGTATGTAATCTATCCTGTAA >Ostrea_lur_contig3 CCCTCTGTCTGTCCTTCCATGCACGCAGGGGGCCCTTGTTAGGTTTATATTGTACGGTAACTCCATCAGGGATCAGGCGCCCGTCCGCTCTCATCACCTCGTACTGAGGCTTCTCCCACTTAGTGAATCCCCACTTCTTGGACACGTGGATCTTCTGACGTCCGGGGAACTTGAACTTGGCTCTCCTGAGTGCTTCTATCACGGCAGCCTGGTGACTCTCACGAGCACGTACAGACATGATTGGCTGTCCTATGTGTACACGGGCTACGGTGCCTTGTGGTTTACCAAAAGCTCCTCTCATTCCCGTCTGAAGCCTATCGGCTCCAGCGCACGACAACATCTTGTTGATTCTGATGACGTGGAAGGGGTGCACTCGAATTCGCATGTGGAAAGCATCTTTACCACAGTTCTTGACCAAATACTTGTTGGCACAGATACGTCCTGCTTCTAGAGCTTCCGAGGAGAGCTGTTCGTACTCATCAGATACGAGATGCACACACAGGGGGAAGTCATCTACCTTGGCCTTCTTCCTCCCAAGATCAAAAATACGGATCTTTGCATCTGGGACACCTCTACAAAATCTGGACTTCGGATAAGGTTTGTTCTTACAGTACCGGTAACACCGAGCTGGTCGGCGTCCCATTTTGAATTAGAA >Ostrea_lur_contig4 CAAAAATATAAGACAAGCGTAATTAAAACCTACTTTTAAAAATGTACATGCTTTATCTACGATAAGCAATAACTTTTAAGCTACATGTATGATACACATTGTTTAGCAGTTACGATTGCATGTATCTCACTATATCTTTTCTCTATTAGCGCCTTACAGATACTCGTCCCGCTTTCGGTTCATCGGTACTTCTTCCTCCAAATTGTCACTTATTGTCTTGTCTTTGGTTTCCTTCAGCAAAAGGCACGTAATTGCAGAGGCCAACATCACAATAAAACATATTATGTACATTACTCCTGGGTTCTCTTTGTTCACAACAACGAGTTGAGGCGCTATCAAAGCTCCTATACGAGAGATCGAGTTTTGGGTTCCATAACCGATGTTCCTGACGACAGTTGGATACACTTCCGTTGTGAAGGCTATGATGGCAGCCCAAGACGCAGAGACACCAAACTTGGCTGCCAG >Ostrea_lur_contig5 CAGCCCAAGTCGAGTGCATTTGGACGATGGAACATATTGGTCAGAAAGAGCAGCGTTATTTCAAGGAAAATCTCATCGACAAGTGTTTAACGACAGCATGAGCAAGCTCTACTCCAAAATGTACCGGAACGCGCTGCGTCCAGGGCCGATCTGATAGTTTATACCTCAGTAGATTCCTCTCAGCTGTGATATTAGATAGTGTCTGTGTATATTTATGATATTTAGGATAAAAGCTATGTGACTCCAGCCATTTCCTGGCACTAAAAGTTTCACTTCAAAACATATGTTGTCTACCATTTTGTCTATTTTTTTATGTTACTAGTGCTCTGTTAACTTTTGATCAGTGAAATTGTTGGTGGCTTTTGATTTGGGGTCTCGGATTCCGTAACTTTTATCCGTGCTTGTTTTGTGTGACAGTACTCGAGTAGTGTGGCCAGTGACACAGAGTTTGTATGGGGGAGGCGGAGTTATCTCTTGCAGGTATCCCAGGGTTCCTCTTACAGGTATCCCAGGATTCCACCTGGTTACCAAACGTCTGACAAATGAAATAAAGCGTATCTTTTGTTTTTGACTGGGTGTAGAGAATCAAAATGTATAATTGCTCCAATATTACAGGGATGTGTATAGCTTTTCAGATTTTAATATAACAATTCCTATTTCCATAAATGTCTCATTTTAGTGTTTTTTTTATTTTATATAATATGCAGCACAAGCCTACACATGATTATATTAATACGGAATCAGCTGGCTTTTATTGTATCACA
!tail /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta
>Ostrea_lur_contig41132 AAATTTATAGGAATCCCCCGTCCACCCACAACTGAGAAAACAGACTTGTTCGATATTGATTTATCACAATGACCGCAACCTTGAAGTGTGAAGTTTCAGATCATGTAGTACAAATCAAAGAAAAAATAGAAATACAAATGCTTGCAAAATGATTTAGATAATCTACCTATTATCTGAGATATATTTGTGGTAAACTAAGTAGTTCATATTTGATATTTTTGGTAAAAATTCAATTTTATTTCTCTGTTTATTTATTTTATTTTTAAAAGTTAGGATGTATTTTCAATACAGTTT >Ostrea_lur_contig41133 GGCTAATACAATATTGGAATCAGTAAACACCTGTACACAAAGTTTAGTGAAAATATGAAATGGCATGTGTCGGCCTTTGTCTGATTATACACTGGACAGCCTCTTTTTTTAAAATGTTTTTAAAATCATTGGTTCTATTGGGAATTTTACAAGGTCGTTTAGAACATAGACGATTTAGTGCCGATAGAAAAGCACTATAAATGTGCACTGGAGAACACGTCTACAATAAGG >Ostrea_lur_contig41134 ATATGAAAAAACAGACAGTCAATAAGGAAGCTCAATTTGTGCCCATGGGAATTCTAAGATCATGACATCAGTTAATGGCCTTATAATTAACAACAAGGCTACATGTACCCCGTTCAAATGGAAAGTAAACAGATATTAGAGACGGAGCGCTTCAACAGTACTATGTTTTACAGCAAGTTTCATAGAAATGTATATTGTCAGTTTTGATGACGTCATGCATCTTGTCAATTACCTTTACTGCTTCGTCTTTTCC >Ostrea_lur_contig41135 GGTAGATCTATCTAATGTTTGGGCTATCAGCTGGCTATCAATGCAATGATGTTCAGTTCTCTAATAATCACGGAGATAGTTTGTGGAAAAGATAGATTATTCATTCTACGGAAGTTGAAATAGATTGATCTATTCATTTCTAAATGTAATCAGGTGATTAGAGGTTTAGTTATACTGATTTAATGTATTCCTGTCAAACAGGTACCCGATGGCTACCTATCA >Ostrea_lur_contig41136 TTTATAAACCTGTAAAATAAGTTTATTCACCAATCGTGGACCCTTTACATGCAATCGTCTAAAACCATTGCCGTTCAATATAGGTATCATCTAGATTTGAAAGTTTGATTTCAGTATTACCGATTTAGCATGGATTATACTGATCTCAAACCGGCCACGATTGTTCTATGGTGACGTCTCCATATGAGTGAAATATTCTCGAGTGGGACGTAAAACAATAA
!tail /Users/sr320/Desktop/0001_DataS1.fa
>Ostrea_lur_contig41132 AAATTTATAGGAATCCCCCGTCCACCCACAACTGAGAAAACAGACTTGTTCGATATTGATTTATCACAATGACCGCAACCTTGAAGTGTGAAGTTTCAGATCATGTAGTACAAATCAAAGAAAAAATAGAAATACAAATGCTTGCAAAATGATTTAGATAATCTACCTATTATCTGAGATATATTTGTGGTAAACTAAGTAGTTCATATTTGATATTTTTGGTAAAAATTCAATTTTATTTCTCTGTTTATTTATTTTATTTTTAAAAGTTAGGATGTATTTTCAATACAGTTT >Ostrea_lur_contig41133 GGCTAATACAATATTGGAATCAGTAAACACCTGTACACAAAGTTTAGTGAAAATATGAAATGGCATGTGTCGGCCTTTGTCTGATTATACACTGGACAGCCTCTTTTTTTAAAATGTTTTTAAAATCATTGGTTCTATTGGGAATTTTACAAGGTCGTTTAGAACATAGACGATTTAGTGCCGATAGAAAAGCACTATAAATGTGCACTGGAGAACACGTCTACAATAAGG >Ostrea_lur_contig41134 ATATGAAAAAACAGACAGTCAATAAGGAAGCTCAATTTGTGCCCATGGGAATTCTAAGATCATGACATCAGTTAATGGCCTTATAATTAACAACAAGGCTACATGTACCCCGTTCAAATGGAAAGTAAACAGATATTAGAGACGGAGCGCTTCAACAGTACTATGTTTTACAGCAAGTTTCATAGAAATGTATATTGTCAGTTTTGATGACGTCATGCATCTTGTCAATTACCTTTACTGCTTCGTCTTTTCC >Ostrea_lur_contig41135 GGTAGATCTATCTAATGTTTGGGCTATCAGCTGGCTATCAATGCAATGATGTTCAGTTCTCTAATAATCACGGAGATAGTTTGTGGAAAAGATAGATTATTCATTCTACGGAAGTTGAAATAGATTGATCTATTCATTTCTAAATGTAATCAGGTGATTAGAGGTTTAGTTATACTGATTTAATGTATTCCTGTCAAACAGGTACCCGATGGCTACCTATCA >Ostrea_lur_contig41136 TTTATAAACCTGTAAAATAAGTTTATTCACCAATCGTGGACCCTTTACATGCAATCGTCTAAAACCATTGCCGTTCAATATAGGTATCATCTAGATTTGAAAGTTTGATTTCAGTATTACCGATTTAGCATGGATTATACTGATCTCAAACCGGCCACGATTGTTCTATGGTGACGTCTCCATATGAGTGAAATATTCTCGAGTGGGACGTAAAACAATAA
#confirmed file in question was published on Figshare and MER Notes.
#not looking good re the word doc and the data.
#will try to blast primers as independant verification
!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
Building a new DB, current time: 07/12/2013 08:23:28 New DB name: /Volumes/Bay3/Software/ncbi-blast-2.2.27+/db/OlyO_transcriptome_v1 New DB title: /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta Sequence type: Nucleotide Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 41136 sequences in 2.70528 seconds.
#query sequence needs to be primers
!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
!head /Volumes/web/cnidarian/OlyO_Chi_primers_blastn1
BagF Ostrea_lur_contig28411 100.00 20 0 0 1 20 308 327 3e-04 38.1 BagR Ostrea_lur_contig28411 100.00 22 0 0 1 22 408 387 3e-05 41.7 HspF Ostrea_lur_contig402 100.00 20 0 0 1 20 1879 1898 3e-04 38.1 HspR Ostrea_lur_contig402 100.00 20 0 0 1 20 2027 2008 3e-04 38.1 U2aF Ostrea_lur_contig2667 100.00 20 0 0 1 20 638 657 3e-04 38.1 U2aR Ostrea_lur_contig2667 100.00 20 0 0 1 20 767 748 3e-04 38.1 PygmF Ostrea_lur_contig95 100.00 20 0 0 1 20 912 931 3e-04 38.1 PygmR Ostrea_lur_contig95 100.00 20 0 0 1 20 1042 1023 3e-04 38.1 IgfrF Ostrea_lur_contig16177 100.00 20 0 0 1 20 1997 2016 3e-04 38.1 IgfrR Ostrea_lur_contig16177 100.00 20 0 0 1 20 2097 2078 3e-04 38.1
!grep "Ostrea_lur_contig28411" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt
Ostrea_lur_contig28411 Q3ZBG5 9.00E-21 BAG2_BOVIN BAG family molecular chaperone regulator 2 OS=Bos taurus PE=2 SV=1
!grep -w "Ostrea_lur_contig402" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt
#need exact mactch to exclude 402X -w
Ostrea_lur_contig402 Q9GKX8 0 HS90B_HORSE Heat shock protein HSP 90-beta OS=Equus caballus GN=HSP90AB1 PE=2 SV=3
!grep -w "Ostrea_lur_contig2667" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt
Ostrea_lur_contig2667 Q3T127 3.00E-104 U2AF4_BOVIN Splicing factor U2AF 26 kDa subunit OS=Bos taurus GN=U2AF1L4 PE=2 SV=1
!grep -w "Ostrea_lur_contig95" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt
Ostrea_lur_contig95 Q9WUB3 0 "PYGM_MOUSE Glycogen phosphorylase, muscle form OS=Mus musculus GN=Pygm PE=1 SV=3"
!grep -w "Ostrea_lur_contig16177" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt
Ostrea_lur_contig16177 Q05688 1.00E-138 IGF1R_BOVIN Insulin-like growth factor 1 receptor (Fragment) OS=Bos taurus GN=IGF1R PE=2 SV=1