a:96:{i:0;a:3:{i:0;s:14:"document_start";i:1;a:0:{}i:2;i:0;}i:1;a:3:{i:0;s:6:"header";i:1;a:3:{i:0;s:27:"2019 blast Practice example";i:1;i:1;i:2;i:0;}i:2;i:0;}i:2;a:3:{i:0;s:12:"section_open";i:1;a:1:{i:0;i:1;}i:2;i:0;}i:3;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:19:"markdowku_headeratx";i:1;b:1;i:2;i:5;i:3;s:30:" # 2019 blast Practice example";}i:2;i:0;}i:4;a:3:{i:0;s:13:"section_close";i:1;a:0:{}i:2;i:31;}i:5;a:3:{i:0;s:6:"header";i:1;a:3:{i:0;s:67:"The location where gene prediction of pearl Exoc7 seems to be wrong";i:1;i:2;i:2;i:31;}i:2;i:31;}i:6;a:3:{i:0;s:12:"section_open";i:1;a:1:{i:0;i:2;}i:2;i:31;}i:7;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:19:"markdowku_headeratx";i:1;b:1;i:2;i:5;i:3;s:71:" ## The location where gene prediction of pearl Exoc7 seems to be wrong";}i:2;i:31;}i:8;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:31;}i:9;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:29:"First of all file preparation";}i:2;i:104;}i:10;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:134;}i:11;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:1633:" echo ">exoc7_pearl atgactctgaaggatgccctcaacaaaagtcacacaaatacaggaaacatgctcacaata cttcaaagctttgaaaatcgtttaaagaagttagagggaacagttgagcctgtttacaat gagacagaaatgctgcggcgcagacaagaaaatatagagaaaactatgacaacactggac aatgtgctgggttactaccatattgctaaagatgtacaagatttgattaaagaaggtcca gtagtttgtggtctggagaagtacctgtctactatggaccggctgctccaagcactgaac tactttaataaacataacccaaccagtctggaagtgacagatgtcatcaaagtatatgat gatggtaaagatacattgaatgcagagttccgtagtttacttggtcgtcactgtcgtccg gtgccggctgttactatactggatttactaggaccagatgaagagttacaaacaatggaa aatgatgcacccatagaacatctgcctgagaaaattgtgaatgatttaaccctcatcgca aagtggctatacaccaatggtaaagctacagagtatatgaaagattacaccaaagtcagg tcccaaatgctcctctactctctgcaggggaactcaataaagcggaaggctaccacggcc ttgatgcagtccccttttgatccaggtcatagaagacaaggctcttataacgaattgaca aaagaggaaagttttgatgttgaaattgatatctacataacagaactaacagcattgctg aaacttattcagaatgaccctgagagatcttcgatgccccgagacggtacagttcatgaa ctgacaaaccataccattatagtactggagcccctgttagattatgctgagacagctggg gccatgttactcacccatggtgaacatgcagttccatctgatgctgtggatgtcaagaaa agtaaactcaagttggctgactatatcactaaggttttgtcagcattaggattaaactta agtaacaaggcagaaacttacagtgatccaatactcagacatgtgttcatgcttaataac tatcactacatactcaagtctttaaaaaggtctggggtattagaattaattcacacatgg aataaagatgtaggacagttttatgaggaccagatacatgaacaaaaaagactttattcc cagagctggagtaaagttctacattttgtactggaaatgaatgagccaatatcccaacaa agaatccagcaaatggagacatcaaagataaaggacaaagaaaagcagaatataaaagac aagttctctggattcaacaaagagttggaagaaatctcacgtgttcagaaagcatacgcc attcctgatccagaactgagggacaatatcaagaaagacaataaagaatatattgtgccg cgatacaagcttttcttagaaaaatttcaacggctgaacttcacaaagaattcagaaaaa tatatgaaatacactgtaaaggatgtggaagaaacacttgataaatttttcgatacttca gcttaa" > exoc7_pearl.fna ";i:1;N;}i:2;i:134;}i:12;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:1639:" ``` echo ">exoc7_pearl atgactctgaaggatgccctcaacaaaagtcacacaaatacaggaaacatgctcacaata cttcaaagctttgaaaatcgtttaaagaagttagagggaacagttgagcctgtttacaat gagacagaaatgctgcggcgcagacaagaaaatatagagaaaactatgacaacactggac aatgtgctgggttactaccatattgctaaagatgtacaagatttgattaaagaaggtcca gtagtttgtggtctggagaagtacctgtctactatggaccggctgctccaagcactgaac tactttaataaacataacccaaccagtctggaagtgacagatgtcatcaaagtatatgat gatggtaaagatacattgaatgcagagttccgtagtttacttggtcgtcactgtcgtccg gtgccggctgttactatactggatttactaggaccagatgaagagttacaaacaatggaa aatgatgcacccatagaacatctgcctgagaaaattgtgaatgatttaaccctcatcgca aagtggctatacaccaatggtaaagctacagagtatatgaaagattacaccaaagtcagg tcccaaatgctcctctactctctgcaggggaactcaataaagcggaaggctaccacggcc ttgatgcagtccccttttgatccaggtcatagaagacaaggctcttataacgaattgaca aaagaggaaagttttgatgttgaaattgatatctacataacagaactaacagcattgctg aaacttattcagaatgaccctgagagatcttcgatgccccgagacggtacagttcatgaa ctgacaaaccataccattatagtactggagcccctgttagattatgctgagacagctggg gccatgttactcacccatggtgaacatgcagttccatctgatgctgtggatgtcaagaaa agtaaactcaagttggctgactatatcactaaggttttgtcagcattaggattaaactta agtaacaaggcagaaacttacagtgatccaatactcagacatgtgttcatgcttaataac tatcactacatactcaagtctttaaaaaggtctggggtattagaattaattcacacatgg aataaagatgtaggacagttttatgaggaccagatacatgaacaaaaaagactttattcc cagagctggagtaaagttctacattttgtactggaaatgaatgagccaatatcccaacaa agaatccagcaaatggagacatcaaagataaaggacaaagaaaagcagaatataaaagac aagttctctggattcaacaaagagttggaagaaatctcacgtgttcagaaagcatacgcc attcctgatccagaactgagggacaatatcaagaaagacaataaagaatatattgtgccg cgatacaagcttttcttagaaaaatttcaacggctgaacttcacaaagaattcagaaaaa tatatgaaatacactgtaaaggatgtggaagaaacacttgataaatttttcgatacttca gcttaa" > exoc7_pearl.fna ```";}i:2;i:134;}i:13;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:710:" echo ">EKC30356.1 Exocyst complex component 7 [Crassostrea gigas] MLTILQSFENRLRKLENTVEPVYNETEMLRRRQENIEKTMVTLDNVLGYYHVGKEVEEFIKEGPHNCGLE KYLSIMDRLVQAHNYFNKHNPTSLELTDVIRVYDDGKEALVIEFRTLLGRHCRPVPPVMVLDMISTDEEL QGSDDIQLEHLPEKILTELSLISTWLFNNTKNTEYMKDYTRSRSSMLIKSLQGHSFKRRAVITLMQSPFD PGNKRQGSHAELPKEENLDVEVDIYITELSALLKLIQSEAQLMSGIIADKHHRSVFDNIIQEGLDSVIKN GELLAVNAKKSIAKHDFINVLSVFPVLKHLRSIKPEFDLTLEGCATPTRAKLTSLLSTLGSTAAKALEEF ALSIKTDPEKASMPKDGTVHELTNRTIIFLEPLQDYADTAGAMLLLHGEQAAPSEAVDPKKSKMRLADYI TKTLSALGLNLTIKAETYSDPTLRPVFMLNNYHYILKSLKRSGLLDLIHTWNKDVGQFYEDRINEQKKLY SESWSRVMHYITEVHEPISQQRIQAMENSKLKDKEKQNIKDKFSGFNKELEDILKIQKGYAIPDPELREQ MKKDNKDFIIPAFRMFLDKFKRLNFTKNPEKYIKYSVQDVAEVVDKLFDMSA" > exoc7_c.gigas.faa ";i:1;N;}i:2;i:1774;}i:14;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:716:" ``` echo ">EKC30356.1 Exocyst complex component 7 [Crassostrea gigas] MLTILQSFENRLRKLENTVEPVYNETEMLRRRQENIEKTMVTLDNVLGYYHVGKEVEEFIKEGPHNCGLE KYLSIMDRLVQAHNYFNKHNPTSLELTDVIRVYDDGKEALVIEFRTLLGRHCRPVPPVMVLDMISTDEEL QGSDDIQLEHLPEKILTELSLISTWLFNNTKNTEYMKDYTRSRSSMLIKSLQGHSFKRRAVITLMQSPFD PGNKRQGSHAELPKEENLDVEVDIYITELSALLKLIQSEAQLMSGIIADKHHRSVFDNIIQEGLDSVIKN GELLAVNAKKSIAKHDFINVLSVFPVLKHLRSIKPEFDLTLEGCATPTRAKLTSLLSTLGSTAAKALEEF ALSIKTDPEKASMPKDGTVHELTNRTIIFLEPLQDYADTAGAMLLLHGEQAAPSEAVDPKKSKMRLADYI TKTLSALGLNLTIKAETYSDPTLRPVFMLNNYHYILKSLKRSGLLDLIHTWNKDVGQFYEDRINEQKKLY SESWSRVMHYITEVHEPISQQRIQAMENSKLKDKEKQNIKDKFSGFNKELEDILKIQKGYAIPDPELREQ MKKDNKDFIIPAFRMFLDKFKRLNFTKNPEKYIKYSVQDVAEVVDKLFDMSA" > exoc7_c.gigas.faa ```";}i:2;i:1774;}i:15;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:1774;}i:16;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:65:"Download the genome of the pearl oyster which you will use later.";}i:2;i:2492;}i:17;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:2558;}i:18;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:107:" wget https://marinegenomics.oist.jp/pearl/download/pfu_genome1.0.fasta.gz gzip -d pfu_genome1.0.fasta.gz ";i:1;N;}i:2;i:2558;}i:19;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:113:" ``` wget https://marinegenomics.oist.jp/pearl/download/pfu_genome1.0.fasta.gz gzip -d pfu_genome1.0.fasta.gz ```";}i:2;i:2558;}i:20;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:2558;}i:21;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:73:"When you're ready, start docker to set up an environment that uses blast.";}i:2;i:2673;}i:22;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:2747;}i:23;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:95:" docker run -it --rm -v $PWD:$PWD -w $PWD quay.io/biocontainers/blast:2.7.1--boost1.64_1 bash ";i:1;N;}i:2;i:2747;}i:24;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:101:" ``` docker run -it --rm -v $PWD:$PWD -w $PWD quay.io/biocontainers/blast:2.7.1--boost1.64_1 bash ```";}i:2;i:2747;}i:25;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:2747;}i:26;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:110:"Entering the above commands will enter the virtual environment available to blast. The amino acid sequence of ";}i:2;i:2850;}i:27;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:19:"```exoc7_c.gigas```";}i:2;i:5;i:3;s:19:"```exoc7_c.gigas```";}i:2;i:2960;}i:28;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:49:" is used as a DB, and the nucleotide sequence of ";}i:2;i:2979;}i:29;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:17:"```exoc7_pearl```";}i:2;i:5;i:3;s:17:"```exoc7_pearl```";}i:2;i:3028;}i:30;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:49:" is used as a query. First, create a database of ";}i:2;i:3045;}i:31;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:19:"```exoc7_c.gigas```";}i:2;i:5;i:3;s:19:"```exoc7_c.gigas```";}i:2;i:3094;}i:32;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:1:".";}i:2;i:3113;}i:33;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:3115;}i:34;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:49:" makeblastdb -in exoc7_c.gigas.faa -dbtype prot ";i:1;N;}i:2;i:3115;}i:35;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:55:" ``` makeblastdb -in exoc7_c.gigas.faa -dbtype prot ```";}i:2;i:3115;}i:36;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:3115;}i:37;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:63:"Next, blastx will be performed with the amino acid sequence of ";}i:2;i:3172;}i:38;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:19:"```exoc7_c.gigas```";}i:2;i:5;i:3;s:19:"```exoc7_c.gigas```";}i:2;i:3235;}i:39;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:32:" as DB, and the DNA sequence of ";}i:2;i:3254;}i:40;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:17:"```exoc7_pearl```";}i:2;i:5;i:3;s:17:"```exoc7_pearl```";}i:2;i:3286;}i:41;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:12:" as a query.";}i:2;i:3303;}i:42;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:3316;}i:43;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:69:" blastx -db exoc7_c.gigas.faa -query exoc7_pearl.fna -num_threads 4 ";i:1;N;}i:2;i:3316;}i:44;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:75:" ``` blastx -db exoc7_c.gigas.faa -query exoc7_pearl.fna -num_threads 4 ```";}i:2;i:3316;}i:45;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:3316;}i:46;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:46:"As a result, the following output is obtained.";}i:2;i:3393;}i:47;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:3440;}i:48;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:3146:" Database: exoc7_c.gigas.faa 1 sequences; 612 total letters Query= exoc7_pearl Length=1566 Score E Sequences producing significant alignments: (Bits) Value EKC30356.1 Exocyst complex component 7 [Crassostrea gigas] 426 6e-148 > EKC30356.1 Exocyst complex component 7 [Crassostrea gigas] Length=612 Score = 426 bits (1096), Expect = 6e-148, Method: Compositional matrix adjust. Identities = 196/259 (76%), Positives = 235/259 (91%), Gaps = 0/259 (0%) Frame = +1 Query 787 IQNDPERSSMPRDGTVHELTNHTIIVLEPLLDYAETAGAMLLTHGEHAVPSDAVDVKKSK 966 I+ DPE++SMP+DGTVHELTN TII LEPL DYA+TAGAMLL HGE A PS+AVD KKSK Sbjct 354 IKTDPEKASMPKDGTVHELTNRTIIFLEPLQDYADTAGAMLLLHGEQAAPSEAVDPKKSK 413 Query 967 LKLADYITKVLSALGLNLSNKAETYSDPILRHVFMLNNYHYILKSLKRSGVLELIHTWNK 1146 ++LADYITK LSALGLNL+ KAETYSDP LR VFMLNNYHYILKSLKRSG+L+LIHTWNK Sbjct 414 MRLADYITKTLSALGLNLTIKAETYSDPTLRPVFMLNNYHYILKSLKRSGLLDLIHTWNK 473 Query 1147 DVGQFYEDQIHEQKRLYSQSWSKVLHFVLEMNEPISQQRIQQMETSKIKDKEKQNIKDKF 1326 DVGQFYED+I+EQK+LYS+SWS+V+H++ E++EPISQQRIQ ME SK+KDKEKQNIKDKF Sbjct 474 DVGQFYEDRINEQKKLYSESWSRVMHYITEVHEPISQQRIQAMENSKLKDKEKQNIKDKF 533 Query 1327 SGFNKELEEISRVQKAYAIPDPELRDNIKKDNKEYIVPRYKLFLEKFQRLNFTKNSEKYM 1506 SGFNKELE+I ++QK YAIPDPELR+ +KKDNK++I+P +++FL+KF+RLNFTKN EKY+ Sbjct 534 SGFNKELEDILKIQKGYAIPDPELREQMKKDNKDFIIPAFRMFLDKFKRLNFTKNPEKYI 593 Query 1507 KYTVKDVEETLDKFFDTSA 1563 KY+V+DV E +DK FD SA Sbjct 594 KYSVQDVAEVVDKLFDMSA 612 Score = 389 bits (998), Expect = 2e-133, Method: Compositional matrix adjust. Identities = 203/341 (60%), Positives = 250/341 (73%), Gaps = 33/341 (10%) Frame = +1 Query 49 MLTILQSFENRLKKLEGTVEPVYNETEMLRRRQENIEKTMTTLDNVLGYYHIAKDVQDLI 228 MLTILQSFENRL+KLE TVEPVYNETEMLRRRQENIEKTM TLDNVLGYYH+ K+V++ I Sbjct 1 MLTILQSFENRLRKLENTVEPVYNETEMLRRRQENIEKTMVTLDNVLGYYHVGKEVEEFI 60 Query 229 KEGPVVCGLEKYLSTMDRLLQALNYFNKHNPTSLEVTDVIKVYDDGKDTLNAEFRSLLGR 408 KEGP CGLEKYLS MDRL+QA NYFNKHNPTSLE+TDVI+VYDDGK+ L EFR+LLGR Sbjct 61 KEGPHNCGLEKYLSIMDRLVQAHNYFNKHNPTSLELTDVIRVYDDGKEALVIEFRTLLGR 120 Query 409 HCRPVPAVTILDLLGPDEELQTMENDAPIEHLPEKIVNDLTLIAKWLYTNGKATEYMKDY 588 HCRPVP V +LD++ DEELQ +D +EHLPEKI+ +L+LI+ WL+ N K TEYMKDY Sbjct 121 HCRPVPPVMVLDMISTDEELQG-SDDIQLEHLPEKILTELSLISTWLFNNTKNTEYMKDY 179 Query 589 TKVRSQMLLYSLQGNSIKRKATTALMQSPFDPGHRRQGSYNELTKEESFDVEIDIYITEL 768 T+ RS ML+ SLQG+S KR+A LMQSPFDPG++RQGS+ EL KEE+ DVE+DIYITEL Sbjct 180 TRSRSSMLIKSLQGHSFKRRAVITLMQSPFDPGNKRQGSHAELPKEENLDVEVDIYITEL 239 Query 769 TALLKLIQNDPERSSMPRDGTVHELTNHTII--VLEPLLDYAETAGAMLLTHGEHAVPSD 942 +ALLKLIQ++ + S G + + + ++ +++ LD G +L Sbjct 240 SALLKLIQSEAQLMS----GIIADKHHRSVFDNIIQEGLDSVIKNGELL----------- 284 Query 943 AVDVKKSKLKLADYITKVLSALGLNLSNKAETYSDPILRHV 1065 AV+ KKS K D+I VLS P+L+H+ Sbjct 285 AVNAKKSIAK-HDFIN-VLSVF-------------PVLKHL 310 ";i:1;N;}i:2;i:3440;}i:49;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:3152:" ``` Database: exoc7_c.gigas.faa 1 sequences; 612 total letters Query= exoc7_pearl Length=1566 Score E Sequences producing significant alignments: (Bits) Value EKC30356.1 Exocyst complex component 7 [Crassostrea gigas] 426 6e-148 > EKC30356.1 Exocyst complex component 7 [Crassostrea gigas] Length=612 Score = 426 bits (1096), Expect = 6e-148, Method: Compositional matrix adjust. Identities = 196/259 (76%), Positives = 235/259 (91%), Gaps = 0/259 (0%) Frame = +1 Query 787 IQNDPERSSMPRDGTVHELTNHTIIVLEPLLDYAETAGAMLLTHGEHAVPSDAVDVKKSK 966 I+ DPE++SMP+DGTVHELTN TII LEPL DYA+TAGAMLL HGE A PS+AVD KKSK Sbjct 354 IKTDPEKASMPKDGTVHELTNRTIIFLEPLQDYADTAGAMLLLHGEQAAPSEAVDPKKSK 413 Query 967 LKLADYITKVLSALGLNLSNKAETYSDPILRHVFMLNNYHYILKSLKRSGVLELIHTWNK 1146 ++LADYITK LSALGLNL+ KAETYSDP LR VFMLNNYHYILKSLKRSG+L+LIHTWNK Sbjct 414 MRLADYITKTLSALGLNLTIKAETYSDPTLRPVFMLNNYHYILKSLKRSGLLDLIHTWNK 473 Query 1147 DVGQFYEDQIHEQKRLYSQSWSKVLHFVLEMNEPISQQRIQQMETSKIKDKEKQNIKDKF 1326 DVGQFYED+I+EQK+LYS+SWS+V+H++ E++EPISQQRIQ ME SK+KDKEKQNIKDKF Sbjct 474 DVGQFYEDRINEQKKLYSESWSRVMHYITEVHEPISQQRIQAMENSKLKDKEKQNIKDKF 533 Query 1327 SGFNKELEEISRVQKAYAIPDPELRDNIKKDNKEYIVPRYKLFLEKFQRLNFTKNSEKYM 1506 SGFNKELE+I ++QK YAIPDPELR+ +KKDNK++I+P +++FL+KF+RLNFTKN EKY+ Sbjct 534 SGFNKELEDILKIQKGYAIPDPELREQMKKDNKDFIIPAFRMFLDKFKRLNFTKNPEKYI 593 Query 1507 KYTVKDVEETLDKFFDTSA 1563 KY+V+DV E +DK FD SA Sbjct 594 KYSVQDVAEVVDKLFDMSA 612 Score = 389 bits (998), Expect = 2e-133, Method: Compositional matrix adjust. Identities = 203/341 (60%), Positives = 250/341 (73%), Gaps = 33/341 (10%) Frame = +1 Query 49 MLTILQSFENRLKKLEGTVEPVYNETEMLRRRQENIEKTMTTLDNVLGYYHIAKDVQDLI 228 MLTILQSFENRL+KLE TVEPVYNETEMLRRRQENIEKTM TLDNVLGYYH+ K+V++ I Sbjct 1 MLTILQSFENRLRKLENTVEPVYNETEMLRRRQENIEKTMVTLDNVLGYYHVGKEVEEFI 60 Query 229 KEGPVVCGLEKYLSTMDRLLQALNYFNKHNPTSLEVTDVIKVYDDGKDTLNAEFRSLLGR 408 KEGP CGLEKYLS MDRL+QA NYFNKHNPTSLE+TDVI+VYDDGK+ L EFR+LLGR Sbjct 61 KEGPHNCGLEKYLSIMDRLVQAHNYFNKHNPTSLELTDVIRVYDDGKEALVIEFRTLLGR 120 Query 409 HCRPVPAVTILDLLGPDEELQTMENDAPIEHLPEKIVNDLTLIAKWLYTNGKATEYMKDY 588 HCRPVP V +LD++ DEELQ +D +EHLPEKI+ +L+LI+ WL+ N K TEYMKDY Sbjct 121 HCRPVPPVMVLDMISTDEELQG-SDDIQLEHLPEKILTELSLISTWLFNNTKNTEYMKDY 179 Query 589 TKVRSQMLLYSLQGNSIKRKATTALMQSPFDPGHRRQGSYNELTKEESFDVEIDIYITEL 768 T+ RS ML+ SLQG+S KR+A LMQSPFDPG++RQGS+ EL KEE+ DVE+DIYITEL Sbjct 180 TRSRSSMLIKSLQGHSFKRRAVITLMQSPFDPGNKRQGSHAELPKEENLDVEVDIYITEL 239 Query 769 TALLKLIQNDPERSSMPRDGTVHELTNHTII--VLEPLLDYAETAGAMLLTHGEHAVPSD 942 +ALLKLIQ++ + S G + + + ++ +++ LD G +L Sbjct 240 SALLKLIQSEAQLMS----GIIADKHHRSVFDNIIQEGLDSVIKNGELL----------- 284 Query 943 AVDVKKSKLKLADYITKVLSALGLNLSNKAETYSDPILRHV 1065 AV+ KKS K D+I VLS P+L+H+ Sbjct 285 AVNAKKSIAK-HDFIN-VLSVF-------------PVLKHL 310 ```";}i:2;i:3440;}i:50;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:3440;}i:51;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:101:"There are two aligned sequences, and looking at the second alignment, “Sbjct” is the sequence of ";}i:2;i:6594;}i:52;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:19:"```exoc7_c.gigas```";}i:2;i:5;i:3;s:19:"```exoc7_c.gigas```";}i:2;i:6695;}i:53;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:33:" used as DB and is homologous to ";}i:2;i:6714;}i:54;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:17:"```exoc7_pearl```";}i:2;i:5;i:3;s:17:"```exoc7_pearl```";}i:2;i:6747;}i:55;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:55:", but the homology after 248 amino acids is low. Since ";}i:2;i:6764;}i:56;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:17:"```exoc7_pearl```";}i:2;i:5;i:3;s:17:"```exoc7_pearl```";}i:2;i:6819;}i:57;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:204:" of the query is a DNA sequence, it increases by 3 bp per character, and the region of 787 bp or later corresponds to a region of low homology. Then, when looking at the first alignment, the alignment of ";}i:2;i:6836;}i:58;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:17:"```exoc7_pearl```";}i:2;i:5;i:3;s:17:"```exoc7_pearl```";}i:2;i:7040;}i:59;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:31:" starts from 787 bp, while the ";}i:2;i:7057;}i:60;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:19:"```exoc7_c.gigas```";}i:2;i:5;i:3;s:19:"```exoc7_c.gigas```";}i:2;i:7088;}i:61;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:93:" starts from 354 amino acids. Therefore, it is understood that the 248 to 353 amino acids of ";}i:2;i:7107;}i:62;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:19:"```exoc7_c.gigas```";}i:2;i:5;i:3;s:19:"```exoc7_c.gigas```";}i:2;i:7200;}i:63;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:26:" are deleted in predicted ";}i:2;i:7219;}i:64;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:20:"markdowku_codespans3";i:1;a:1:{i:0;s:17:"```exoc7_pearl```";}i:2;i:5;i:3;s:17:"```exoc7_pearl```";}i:2;i:7245;}i:65;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:1:".";}i:2;i:7262;}i:66;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:7264;}i:67;a:3:{i:0;s:13:"section_close";i:1;a:0:{}i:2;i:7264;}i:68;a:3:{i:0;s:6:"header";i:1;a:3:{i:0;s:99:"Investigate which scaffold of the pearl oyster genome has the deleted sequences in gene prediction.";i:1;i:2;i:2;i:7264;}i:2;i:7264;}i:69;a:3:{i:0;s:12:"section_open";i:1;a:1:{i:0;i:2;}i:2;i:7264;}i:70;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:19:"markdowku_headeratx";i:1;b:1;i:2;i:5;i:3;s:103:" ## Investigate which scaffold of the pearl oyster genome has the deleted sequences in gene prediction.";}i:2;i:7264;}i:71;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:7264;}i:72;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:54:"First, the deleted sequence is stored in FASTA format.";}i:2;i:7369;}i:73;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:7424;}i:74;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:151:" echo ">exoc7_deleted SEAQLMSGIIADKHHRSVFDNIIQEGLDSVIKNGELLAVNAKKSIAKHDFINVLSVFPVLKHLRSIKPEFDLTLEGCATPTRAKLTSLLSTLGSTAAKALEEFALS" > exoc7_deleted.faa ";i:1;N;}i:2;i:7424;}i:75;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:157:" ``` echo ">exoc7_deleted SEAQLMSGIIADKHHRSVFDNIIQEGLDSVIKNGELLAVNAKKSIAKHDFINVLSVFPVLKHLRSIKPEFDLTLEGCATPTRAKLTSLLSTLGSTAAKALEEFALS" > exoc7_deleted.faa ```";}i:2;i:7424;}i:76;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:7424;}i:77;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:54:"Next, create a blast index of the pearl oyster genome.";}i:2;i:7583;}i:78;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:7638;}i:79;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:51:" makeblastdb -in pfu_genome1.0.fasta -dbtype nucl ";i:1;N;}i:2;i:7638;}i:80;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:57:" ``` makeblastdb -in pfu_genome1.0.fasta -dbtype nucl ```";}i:2;i:7638;}i:81;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:7638;}i:82;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:83:"Search the pearl oyster genome with tblastn, using the deleted sequence as a query.";}i:2;i:7697;}i:83;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:7781;}i:84;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:74:" tblastn -db pfu_genome1.0.fasta -query exoc7_deleted.faa -num_threads 4 ";i:1;N;}i:2;i:7781;}i:85;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:80:" ``` tblastn -db pfu_genome1.0.fasta -query exoc7_deleted.faa -num_threads 4 ```";}i:2;i:7781;}i:86;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:7781;}i:87;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:12:"As a result,";}i:2;i:7863;}i:88;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:7876;}i:89;a:3:{i:0;s:4:"code";i:1;a:2:{i:0;s:806:" Query= exoc7_deleted Length=106 Score E Sequences producing significant alignments: (Bits) Value scaffold294819.1|size544 118 2e-33 > scaffold294819.1|size544 Length=544 Score = 118 bits (295), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 55/75 (73%), Positives = 67/75 (89%), Gaps = 0/75 (0%) Frame = -3 Query 1 SEAQLMSGIIADKHHRSVFDNIIQEGLDSVIKNGELLAVNAKKSIAKHDFINVLSVFPVL 60 SEAQLMSGII +KHHRSVF++II+ LD V+K GE LA NAKKSI+KHDF++VLSVFPV+ Sbjct 227 SEAQLMSGIIPEKHHRSVFESIIEGSLDMVVKGGETLASNAKKSISKHDFLSVLSVFPVV 48 Query 61 KHLRSIKPEFDLTLE 75 +HLR++KPEFDL LE Sbjct 47 RHLRTVKPEFDLALE 3 ";i:1;N;}i:2;i:7876;}i:90;a:3:{i:0;s:6:"plugin";i:1;a:4:{i:0;s:26:"markdowku_githubcodeblocks";i:1;b:1;i:2;i:5;i:3;s:812:" ``` Query= exoc7_deleted Length=106 Score E Sequences producing significant alignments: (Bits) Value scaffold294819.1|size544 118 2e-33 > scaffold294819.1|size544 Length=544 Score = 118 bits (295), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 55/75 (73%), Positives = 67/75 (89%), Gaps = 0/75 (0%) Frame = -3 Query 1 SEAQLMSGIIADKHHRSVFDNIIQEGLDSVIKNGELLAVNAKKSIAKHDFINVLSVFPVL 60 SEAQLMSGII +KHHRSVF++II+ LD V+K GE LA NAKKSI+KHDF++VLSVFPV+ Sbjct 227 SEAQLMSGIIPEKHHRSVFESIIEGSLDMVVKGGETLASNAKKSISKHDFLSVLSVFPVV 48 Query 61 KHLRSIKPEFDLTLE 75 +HLR++KPEFDL LE Sbjct 47 RHLRTVKPEFDLALE 3 ```";}i:2;i:7876;}i:91;a:3:{i:0;s:6:"p_open";i:1;a:0:{}i:2;i:7876;}i:92;a:3:{i:0;s:5:"cdata";i:1;a:1:{i:0;s:143:"is obtained, and it can be seen that there is one Exoc7 exon in the scaffold 29491. 1 (Exon of Exoc7 other than this exon is in scaffold 1200).";}i:2;i:8690;}i:93;a:3:{i:0;s:7:"p_close";i:1;a:0:{}i:2;i:8833;}i:94;a:3:{i:0;s:13:"section_close";i:1;a:0:{}i:2;i:8834;}i:95;a:3:{i:0;s:12:"document_end";i:1;a:0:{}i:2;i:8834;}}