{"id":2901,"date":"2019-05-19T02:33:44","date_gmt":"2019-05-18T18:33:44","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2901"},"modified":"2019-05-19T18:05:36","modified_gmt":"2019-05-19T10:05:36","slug":"rfam%e6%95%b0%e6%8d%ae%e5%ba%93%e7%9a%84small-nuclear-rna%e5%88%86%e7%b1%bb%e7%bb%9f%e8%ae%a1","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2901","title":{"rendered":"Rfam\u6570\u636e\u5e93\u7684Small nuclear RNA\u5206\u7c7b\u7edf\u8ba1"},"content":{"rendered":"\n

\u5e38\u89c1\u7684Non-coding RNA\u57fa\u56e0\u4e3b\u8981\u5206\u56db\u7c7b\uff1arRNA\u57fa\u56e0\u3001tRNA\u57fa\u56e0\u3001snRNA\u57fa\u56e0\u548cmiRNA\u57fa\u56e0\u3002tRNA\u57fa\u56e0\u4e00\u822c\u4f7f\u7528tRNAScan-SE\u8f6f\u4ef6\u8fdb\u884c\u5206\u6790\uff1brRNA\u57fa\u56e0\u4e00\u822c\u4f7f\u7528RNAmmer\u8f6f\u4ef6\u6216BLAST\u8f6f\u4ef6\u8fdb\u884c\u5206\u6790\uff1b\u5bf9\u4e8esnRNA\u57fa\u56e0\u548cmiRNA\u57fa\u56e0\uff0c\u5219\u4f7f\u7528Infernal\u8f6f\u4ef6\u5c06\u57fa\u56e0\u7ec4\u5e8f\u5217\u6bd4\u5bf9\u5230Rfam\u6570\u636e\u5e93\u8fdb\u884c\u5206\u6790\u5f97\u5230\u3002\u4f46Rfam\u6570\u636e\u5e93\u5206\u6790\u80fd\u5f97\u5230\u5f88\u591aNon-conding RNA\u4fe1\u606f\uff0c\u63d0\u53d6\u5176\u4e2d\u7684snRNA\u4fe1\u606f\u5219\u6709\u70b9\u9ebb\u70e6\u3002\u5177\u4f53\u5206\u6790\u65b9\u6cd5\u5982\u4e0b:<\/p>\n\n\n\n

1. snRNA\u7b80\u4ecb<\/h2>\n\n\n\n

snRNA\u4e00\u7c7b\u8f83\u5c0f\u7684\u5b58\u5728\u7ec6\u80de\u6838\u4e2d\u7684RNA\u5206\u5b50\uff0c\u901a\u5e38~150\u4e2a\u6838\u82f7\u9178\u957f\u5ea6\u3002\u53ef\u4ee5\u5206\u6210\u56db\u7c7b\uff1a<\/p>\n\n\n\n

1. Sm-class snRNA: \u7531RNA\u805a\u5408\u9176II\u8f6c\u5f55\uff0c\u5305\u542bU1, U2, U4, U4atac, U5, U7, U11,\u548cU12\u51e0\u7c7b\u3002\u8be5\u7c7bsnRNA\u80fd\u4ece\u6838\u5b54\u8f6c\u79fb\u5230\u7ec6\u80de\u8d28\u4e2d\uff0c\u6700\u540e\u5f62\u6210splicesome\uff0c\u7528\u4e8e\u5bf9mRNA\u524d\u4f53\u8fdb\u884c\u52a0\u5de5\uff0c\u53bb\u9664introns\u3002

2. Lsm-class snRNA\uff1a\u548c\u7b2c\u4e00\u7c7bsnRNA\u7c7b\u4f3c\uff0c\u4f46\u7531RNA\u805a\u5408\u9176III\u8f6c\u5f55\uff0c\u4e0d\u4f1a\u79bb\u5f00\u7ec6\u80de\u6838\u3002

3. C\/D box snoRNA: \u5b58\u5728\u6838\u4ec1\u4e2d\u7684RNA\u5206\u5b50\uff0c\u5305\u542b\u4e24\u4e2a\u4fdd\u5b88\u7684\u5e8f\u5217motifs\uff0cC (RUGAUGA) and D (CUGA)\uff0c\u901a\u5e38\u80fd\u5bf9rRNA\u8fdb\u884c\u7532\u57fa\u5316\u52a0\u5de5\u3002

4. H\/ACA box snoRNA\uff1a\u5b58\u5728\u6838\u4ec1\u4e2d\u7684RNA\u5206\u5b50\uff0c\u5305\u542b\u4e24\u4e2a\u4fdd\u5b88\u7684\u5e8f\u5217motifs\uff0cH box (consensus ANANNA) and the ACA box (ACA)\uff0c\u901a\u5e38\u80fd\u5bf9tRNA\u8fdb\u884c\u5047\u5c3f\u82f7\u5316\u52a0\u5de5\u3002
<\/pre>\n\n\n\n
2. snoRNA\u5206\u7c7b\u548cRF\u7f16\u53f7\u7684\u83b7\u53d6<\/h2>\n\n\n\n
\u76f8\u6bd4\u4e8esnRNA\uff0csnoRNA\u5bb6\u65cf\u5e9e\u5927\u3002\u82e5\u9700\u8981\u7edf\u8ba1snoRNA\u4fe1\u606f\uff0c\u9996\u5148\u9700\u8981\u4e86\u89e3\u90a3\u4e9bRfam\u4e2d\u7684\u7f16\u53f7\u5c5e\u4e8e\u90a3\u79cd\u7c7b\u578b\u7684snoRNA\u3002<\/p>\n\n\n\n
\u5728Rfam\u6570\u636e\u5e93\u6587\u4ef6Rfam.cm\u4e2d\u4ee5\u5173\u952e\u8bcdSmall nucleolar RNA\u641c\u7d22\uff0c\u4ece\u800c\u786e\u5b9a\u5c5e\u4e8esnoRNA\u7684Rfam\u7f16\u53f7\u3002<\/p>\n\n\n\n
perl -e '$\/ = \"\\n\/\/\"; while (<>) { if (m\/Small nucleolar RNA\/i) { my $name = $1 if m\/NAME\\s+(\\S+)\/; my $acc = $1 if m\/ACC\\s+(\\S+)\/; print \"$acc\\t$name\\n\"; } }' Rfam.cm > snoRNA_1.list<\/code><\/pre>\n\n\n\n
\u7136\u540e\uff0c\u6839\u636eRfam\u7f16\u53f7\u5728Rfam\u7f51\u7ad9\u4e2d\u9274\u5b9a\u6240\u5c5e\u7684snoRNA\u5206\u7c7b\uff0cC\/D box\u6216 H\/ACA box\u3002\u6b64\u6b65\u9aa4\u9700\u8981\u7f16\u5199\u5982\u4e0b\u7a0b\u5e8fsnoRNA_type.pl\uff0c\u6765\u81ea\u52a8\u4e0b\u8f7d\u76f8\u5e94Rfam\u7f16\u53f7\u7684\u7f51\u9875\u4fe1\u606f\uff0c\u5e76\u89e3\u6790\u5176\u6240\u5c5e\u5206\u7c7b\u3002<\/p>\n\n\n\n
#!\/usr\/bin\/perl\nuse strict;\n\nmy $info = `curl http:\/\/rfam.xfam.org\/family\/$ARGV[0]`;\n\nif ($info =~ m\/Gene; snRNA; snoRNA; ([^\\s;]+)\/) {\n    print \"$ARGV[0]\\t$1\\n\";\n}\nelse {\n    print \"$ARGV[0]\\tother\\n\";\n}<\/code><\/pre>\n\n\n\n
\u6279\u91cf\u5316\u8fd0\u884c\u89e3\u6790\u7a0b\u5e8f\uff0c\u5e76\u5408\u5e76\u7ed3\u679c\u5f97\u5230snoRNA\u7684Rfam\u7f16\u53f7\u548c\u5206\u7c7b\u4fe1\u606f\u3002<\/p>\n\n\n\n
for i in `cut -f 1 snoRNA_1.list`\ndo\n    echo \"perl snoRNA_type.pl $i > $i.type\"\ndone > command.snoRNA_type.list\nParaFly -c command.snoRNA_type.list -CPU 50\n\ncat *.type > snoRNA_2.list\nrm *.type<\/code><\/pre>\n\n\n\n
cut -f 2 snoRNA_1.list > aa\npaste snoRNA_2.list aa > snoRNA.list\nrm aa snoRNA_1.list snoRNA_2.list snoRNA_type.pl<\/code><\/pre>\n\n\n\n
3. \u7f16\u5199\u7a0b\u5e8f\u7edf\u8ba1snRNA\u4fe1\u606f<\/h2>\n\n\n\n
\u7a0b\u5e8f\u540d\u79f0\uff1asnRNA_stats_from_Rfam.pl <\/p>\n\n\n\n
#!\/usr\/bin\/perl\nuse strict;\nuse Getopt::Long;\n\nmy $usage = <<USAGE;\nUsage:\n    $0 [options] rfam_out.tab snoRNA_type.txt\n\n    --out-prefix <string>    default: snRNA_out\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u524d\u7f00\u3002\u9ed8\u8ba4\u8f93\u51fa\u6587\u4ef6\uff1a\n    \uff081\uff09snRNA_out.stats \u5bf9\u5404\u7c7bsnRNA\u7684\u7edf\u8ba1\u4fe1\u606f\u3002\n    \uff082\uff09snRNA_out.txt \u5bf9Rfam\u6570\u636e\u5e93\u8fdb\u884cInfernal\u5206\u6790\u4e2d\u5c5e\u4e8esnRNA\u7684\u8868\u683c\u7ed3\u679c\u3002\n    \uff083\uff09snRNA_out.gff3 \u5c06\u7b2c2\u4e2a\u7ed3\u679c\u8f6c\u6362\u4e3aGFF3\u683c\u5f0f\u7684\u7ed3\u679c\u3002\n\n    \u7a0b\u5e8f\u901a\u8fc7\u8bfb\u53d6Rfam\u7684infernal\u5206\u6790\u7ed3\u679c\uff0c\u7edf\u8ba1\u51fasmall nuclear RNA\u7684\u4fe1\u606f\u3002snRNA_out.stat\u7ed3\u679c\u6587\u4ef6\u5305\u542b\u591a\u5217\uff1a\n    \u7b2c1\u5217\uff1asnRNA\u5206\u7c7b\n    \u7b2c2\u5217\uff1asnRNA\u540d\u79f0\n    \u7b2c2\u5217\uff1aRF\u7f16\u53f7\n    \u7b2c3\u5217\uff1a\u57fa\u56e0\u5bb6\u65cf\u6570\u91cf\n    \u7b2c4\u5217\uff1a\u5e8f\u5217\u5e73\u5747\u957f\u5ea6\n    \u7b2c5\u5217\uff1a\u5e8f\u5217\u603b\u957f\u5ea6\n\n    small nuclear RNA\u5206\u56db\u5927\u7c7b\uff1a\n    Sm-class snRNA: (U1, U2, U4, U4atac, U5, U6, U7, U11, U12)\n    Lsm-class snRNA: (U6, U6atac)\n    C\/D box snoRNA\n    H\/ACA box snoRNA\n\n    snoRNA\u662f\u6700\u590d\u6742\u7684\u4e00\u7c7b\uff0c\u5728Rfam v14.1\u4e2d\u5305\u542b565\u4e2a\u5bb6\u65cf\uff0c\u5176\u4e2d388\u4e2a\u5c5e\u4e8eC\/D box\uff0c177\u4e2a\u5c5e\u4e8eH\/ACA box\u3002\u901a\u8fc7\u8bfb\u53d6snoRNA_type.txt\u6587\u4ef6\u4e2dRF\u7f16\u53f7\u548csnoRNA\u5206\u7c7b\u5bf9\u5e94\u7684\u4fe1\u606f\uff0c\u6765\u7edf\u8ba1\u4e24\u7c7bsnoRNA\u7684\u6570\u91cf\u3002\n\nUSAGE\nif (@ARGV==0){die $usage}\n\nmy ($out_prefix);\nGetOptions(\n    \"out-prefix:s\" => \\$out_prefix,\n);\n$out_prefix ||= \"snRNA_out\";\n\n# Sm-class\u6216Lsm-class\u7c7b\u578b\u7684snRNA\u5728Rfam\u6570\u636e\u5e93\u4e2d\u540d\u79f0\u548cRF\u7f16\u53f7\u83b7\u53d6\uff1a\n# perl -e '$\/ = \"\\n\/\/\"; while (<>) { if (m\/small nuclear RNA\/i or m\/spliceosomal RNA\/i) { my $name = $1 if m\/NAME\\s+(\\S+)\/; my $acc = $1 if m\/ACC\\s+(\\S+)\/; print \"$acc\\t$name\\n\"; } }' Rfam.cm | uniq\n\nmy %snRNA_RF2Name = (\n    \"RF00003\" => \"U1\",\n    \"RF00004\" => \"U2\",\n    \"RF00007\" => \"U12\",\n    \"RF00015\" => \"U4\",\n    \"RF00020\" => \"U5\",\n    \"RF00026\" => \"U6\",\n    \"RF00066\" => \"U7\",\n    \"RF00488\" => \"U1_yeast\",\n    \"RF00548\" => \"U11\",\n    \"RF00618\" => \"U4atac\",\n    \"RF00619\" => \"U6atac\",\n    \"RF01844\" => \"SmY\",\n    \"RF02491\" => \"Gl_U1\",\n    \"RF02492\" => \"Gl_U2\",\n    \"RF02493\" => \"Gl_U4\",\n    \"RF02494\" => \"Gl_U6\"\n);\n\nmy %snRNA_RF2Class = (\n    \"RF00003\" => \"Sm-class snRNA\",\n    \"RF00004\" => \"Sm-class snRNA\",\n    \"RF00007\" => \"Sm-class snRNA\",\n    \"RF00015\" => \"Sm-class snRNA\",\n    \"RF00020\" => \"Sm-class snRNA\",\n    \"RF00026\" => \"Lsm-class snRNA\",\n    \"RF00066\" => \"Sm-class snRNA\",\n    \"RF00488\" => \"Sm-class snRNA\",\n    \"RF00548\" => \"Sm-class snRNA\",\n    \"RF00618\" => \"Sm-class snRNA\",\n    \"RF00619\" => \"Lsm-class snRNA\",\n    \"RF01844\" => \"Sm-class snRNA\",\n    \"RF02491\" => \"Sm-class snRNA\",\n    \"RF02492\" => \"Sm-class snRNA\",\n    \"RF02493\" => \"Sm-class snRNA\",\n    \"RF02494\" => \"Sm-class snRNA\"\n);\n\nopen IN, $ARGV[1] or die \"Can not open file $ARGV[1], $!\\n\";\nwhile (<IN>) {\n    next if m\/^#\/;\n    next if m\/^\\s*$\/;\n    chomp;\n    @_ = split \/\\t\/;\n    $snRNA_RF2Name{$_[0]} = $_[2];\n\n    if ($_[1] eq \"CD-box\") {\n        $snRNA_RF2Class{$_[0]} = 'C\/D box snoRNA';\n    }\n    elsif ($_[1] eq \"HACA-box\") {\n        $snRNA_RF2Class{$_[0]} = 'H\/ACA box snoRNA';\n    }\n    else {\n        $snRNA_RF2Class{$_[0]} = 'other';\n    }\n}\nclose IN;\n\nmy %class;\nforeach (keys %snRNA_RF2Class) {\n    $class{$snRNA_RF2Class{$_}}{$_} = 1;\n}\n\nopen OUT1, \">\", \"$out_prefix.txt\" or die \"Can not create file $out_prefix.txt, $!\\n\";\nopen OUT2, \">\", \"$out_prefix.gff3\" or die \"Can not create file $out_prefix.gff3, $!\\n\";\nopen OUT3, \">\", \"$out_prefix.stats\" or die \"Can not create file $out_prefix.stats, $!\\n\";\nmy (%stats, %gff3, $total_snRNA_number);\nopen IN, $ARGV[0] or die \"Can not open file $ARGV[0], $!\\n\";\nwhile (<IN>) {\n    if (m\/^#\/) { print OUT1; next; }\n    next if m\/^\\s*$\/;\n\n    @_ = split \/\\s+\/;\n    if (exists $snRNA_RF2Name{$_[3]}) {\n        $total_snRNA_number ++;\n        print OUT1;\n        $gff3{$_} = 1;\n\n        $stats{$_[3]}{\"num\"} ++;\n        $stats{$_[3]}{\"total_length\"} += (abs($_[8] - $_[7]) + 1);\n    }\n}\nclose IN;\n\nmy @class = (\"Sm-class snRNA\", \"Lsm-class snRNA\", 'C\/D box snoRNA', 'H\/ACA box snoRNA');\npush @class, \"other\" if exists $class{\"other\"};\nforeach my $class (@class) {\n    my @rf = keys %{$class{$class}};\n    my (%out1 , %out2);\n    foreach (keys %{$class{$class}}) {\n        my $num = $stats{$_}{\"num\"};\n        next unless $num;\n        my $total_length = $stats{$_}{\"total_length\"};\n        my $avg = int(($total_length \/ $num) * 100 + 0.5) \/ 100;\n        my $out = \"$class\\t$snRNA_RF2Name{$_}\\t$_\\t$num\\t$avg\\t$total_length\";\n        $out1{$out} = $num;\n        $out2{$out} = $total_length;\n    }\n    foreach (sort {$out1{$b} <=> $out1{$a} or $out2{$b} <=> $out2{$a}} keys %out1) {\n        print OUT3 \"$_\\n\";\n    }\n}\n\nmy (%sortGFF1, %sortGFF2, %sortGFF3, %sortGFF4, %gff3_name, %gff3_RF, $number);\nforeach (keys %gff3) {\n    @_ = split \/\\s+\/, $_;\n    my ($seqID, $start, $end, $score, $strand, $name, $rf_code) = ($_[0], $_[7], $_[8], $_[14], $_[9], $_[2], $_[3]);\n    if ($start > $end) {\n        my $tmp_vaule = $start;\n        $start = $end;\n        $end = $tmp_vaule;\n    }\n\n    my $out = \"$seqID\\t.\\tsnRNA\\t$start\\t$end\\t$score\\t$strand\\t\\.\";\n    $sortGFF1{$out} = $seqID;\n    $sortGFF2{$out} = $start;\n    $sortGFF3{$out} = $end;\n    $sortGFF4{$out} = $strand;\n    $gff3_name{$out} = $name;\n    $gff3_RF{$out} = $rf_code;\n}\n\nforeach (sort {$sortGFF1{$a} cmp $sortGFF1{$b} or $sortGFF2{$a} <=> $sortGFF2{$b} or $sortGFF3{$a} <=> $sortGFF3{$b} or $sortGFF4{$a} cmp $sortGFF4{$b}} keys %sortGFF1) {\n    $number ++;\n    my $id = '0' x (length($total_snRNA_number) - length($number)) . $number;\n    print OUT2 \"$_\\tID=snRNA_$id;Name=$gff3_name{$_};RF=$gff3_RF{$_}\\n\";\n}\nclose OUT1; close OUT2; close OUT3;<\/code><\/pre>\n\n\n\n
 4. \u7f16\u5199\u7a0b\u5e8f\u7edf\u8ba1miRNA\u4fe1\u606f <\/h2>\n\n\n\n
\u7a0b\u5e8f\u540d\u79f0\uff1amiRNA_stats_from_Rfam.pl<\/p>\n\n\n\n
#!\/usr\/bin\/perl\nuse strict;\nuse Getopt::Long;\n\nmy $usage = <<USAGE;\nUsage:\n    $0 [options] rfam_out.tab Rfam.cm\n\n    --out-prefix <string>    default: miRNA_out\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u524d\u7f00\u3002\u9ed8\u8ba4\u8f93\u51fa\u6587\u4ef6\uff1a\n    \uff081\uff09miRNA_out.stats \u5bf9\u5404\u7c7bmicroRNA\u7684\u7edf\u8ba1\u4fe1\u606f\u3002\n    \uff082\uff09miRNA_out.txt \u5bf9Rfam\u6570\u636e\u5e93\u8fdb\u884cInfernal\u5206\u6790\u4e2d\u5c5e\u4e8emicroRNA\u7684\u8868\u683c\u7ed3\u679c.\n    \uff083\uff09miRNA_out.gff3 \u5c06\u7b2c2\u4e2a\u7ed3\u679c\u8f6c\u6362\u4e3aGFF3\u683c\u5f0f\u7684\u7ed3\u679c\u3002\n\n    \u7a0b\u5e8f\u901a\u8fc7\u8bfb\u53d6Rfam\u6570\u636e\u5e93\u4fe1\u606f\uff0c\u4f7f\u7528\u5173\u952e\u8bcdmicroRNA\u641c\u7d22\uff0c\u627e\u5230\u5c5e\u4e8emiRNA\u7684\u7f16\u53f7\uff0c\u518d\u5206\u6790infernal\u7ed3\u679c\u6587\u4ef6\uff0c\u7edf\u8ba1miRNA\u4fe1\u606f\u3002\n\nUSAGE\nif (@ARGV==0){die $usage}\n\nmy ($out_prefix);\nGetOptions(\n    \"out-prefix:s\" => \\$out_prefix,\n);\n$out_prefix ||= \"miRNA_out\";\n\nopen IN, $ARGV[1] or die \"Can not open file $ARGV[1], $!\\n\";\nmy %miRNA_RF2Name;\n$\/ = \"\\n\/\/\";\nwhile (<IN>) {\n    if (m\/microRNA\/i) {\n        my $name = $1 if m\/NAME\\s+(\\S+)\/;\n        my $acc = $1 if m\/ACC\\s+(\\S+)\/;\n        $miRNA_RF2Name{$acc} = $name;\n    }\n}\nclose IN;\n$\/ = \"\\n\";\n\nopen OUT1, \">\", \"$out_prefix.txt\" or die \"Can not create file $out_prefix.txt, $!\\n\";\nopen OUT2, \">\", \"$out_prefix.gff3\" or die \"Can not create file $out_prefix.gff3, $!\\n\";\nopen OUT3, \">\", \"$out_prefix.stats\" or die \"Can not create file $out_prefix.stats, $!\\n\";\nmy (%stats, %gff3, $total_miRNA_number);\nopen IN, $ARGV[0] or die \"Can not open file $ARGV[0], $!\\n\";\nwhile (<IN>) {\n    if (m\/^#\/) { print OUT1; next; }\n    next if m\/^\\s*$\/;\n\n    @_ = split \/\\s+\/;\n    if (exists $miRNA_RF2Name{$_[3]}) {\n        $total_miRNA_number ++;\n        print OUT1;\n        $gff3{$_} = 1;\n\n        $stats{$_[3]}{\"num\"} ++;\n        $stats{$_[3]}{\"total_length\"} += (abs($_[8] - $_[7]) + 1);\n    }\n}\nclose IN;\n\nforeach (sort {$stats{$b}{\"num\"} <=> $stats{$a}{\"num\"}} keys %stats) {\n    my $num = $stats{$_}{\"num\"};\n    next unless $num;\n    my $total_length = $stats{$_}{\"total_length\"};\n    my $avg = int(($total_length \/ $num) * 100 + 0.5) \/ 100;\n    print OUT3 \"$miRNA_RF2Name{$_}\\t$_\\t$num\\t$avg\\t$total_length\\n\";\n}\n\nmy (%sortGFF1, %sortGFF2, %sortGFF3, %sortGFF4, %gff3_name, %gff3_RF, $number);\nforeach (keys %gff3) {\n    @_ = split \/\\s+\/, $_;\n    my ($seqID, $start, $end, $score, $strand, $name, $rf_code) = ($_[0], $_[7], $_[8], $_[14], $_[9], $_[2], $_[3]);\n    if ($start > $end) {\n        my $tmp_vaule = $start;\n        $start = $end;\n        $end = $tmp_vaule;\n    }\n\n    my $out = \"$seqID\\t.\\tmiRNA\\t$start\\t$end\\t$score\\t$strand\\t\\.\";\n    $sortGFF1{$out} = $seqID;\n    $sortGFF2{$out} = $start;\n    $sortGFF3{$out} = $end;\n    $sortGFF4{$out} = $strand;\n    $gff3_name{$out} = $name;\n    $gff3_RF{$out} = $rf_code;\n}\n\nforeach (sort {$sortGFF1{$a} cmp $sortGFF1{$b} or $sortGFF2{$a} <=> $sortGFF2{$b} or $sortGFF3{$a} <=> $sortGFF3{$b} or $sortGFF4{$a} cmp $sortGFF4{$b}} keys %sortGFF1) {\n    $number ++;\n    my $id = '0' x (length($total_miRNA_number) - length($number)) . $number;\n    print OUT2 \"$_\\tID=miRNA_$id;Name=$gff3_name{$_};RF=$gff3_RF{$_}\\n\";\n}\nclose OUT1; close OUT2; close OUT3;<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
\u5e38\u89c1\u7684Non-coding RNA\u57fa\u56e0\u4e3b\u8981\u5206\u56db\u7c7b\uff1arRNA\u57fa\u56e0\u3001tRNA\u57fa\u56e0\u3001s … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2901"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2901"}],"version-history":[{"count":8,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2901\/revisions"}],"predecessor-version":[{"id":2912,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2901\/revisions\/2912"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2901"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2901"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2901"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}