{"id":2325,"date":"2015-08-25T16:57:01","date_gmt":"2015-08-25T08:57:01","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2325"},"modified":"2015-08-25T16:57:01","modified_gmt":"2015-08-25T08:57:01","slug":"%e4%bd%bf%e7%94%a8-snoscan-%e5%92%8c-snogps-%e8%bf%9b%e8%a1%8c-snornas-%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2325","title":{"rendered":"\u4f7f\u7528 snoscan \u548c snoGPS \u8fdb\u884c snoRNAs \u5206\u6790"},"content":{"rendered":"<h1>1. snoscan \u548c snoGPS \u7b80\u4ecb<\/h1>\n<p>snoRNAs \u4e3b\u8981\u6709 2 \u79cd\u4e0d\u540c\u7c7b\u578b\u3002\u5176\u4e2d C\/D box \u7c7b\u578b snoRNAs \u7528\u4e8e\u6307\u5bfc\u7532\u57fa\u5316\u4fee\u9970(2&#8217;O-ribose-methylations)\uff0c\u8be5\u7532\u57fa\u5316\u4fee\u9970\u4f4d\u4e8e\u6838\u7cd6\u4f53 2&#8242;-OH\u4e0a\uff1b H\/ACA box \u7c7b\u578b snoRNAs \u7528\u4e8e\u6307\u5bfc\u5047\u5c3f\u82f7\u9178\u5316\u4fee\u9970(Pseudouridylation)\uff0c\u5373\u5c06\u5c3f\u5627\u5576\u8f6c\u6362\u4e3a\u5047\u5c3f\u5627\u5576\u3002<\/p>\n<p>snoscan\u7528\u4e8e\u9274\u5b9a C\/D box \u7c7b\u578b snoRNAs\uff1b snoGPS\u7528\u4e8e\u9274\u5b9a H\/ACA box \u7c7b\u578b\u7684 snoRNAs\u3002<\/p>\n<p>\u53ef\u4ee5\u4f7f\u7528<a href=\"http:\/\/lowelab.ucsc.edu\/snoscan\/\" target=\"_blank\">Snoscan Server 1.0 \u7f51\u9875\u5de5\u5177<\/a>\u548c<a href=\"http:\/\/lowelab.ucsc.edu\/snoGPS\/\" target=\"_blank\">snoGPS Server 1.0 \u7f51\u9875\u5de5\u5177<\/a>\u8fdb\u884c snoRNAs \u9884\u6d4b\u3002\u7f51\u9875\u5de5\u5177\u652f\u6301\u7684\u6700\u957f\u5e8f\u5217\u957f\u5ea6\u4e3a 100kb \u3002<\/p>\n<h1>2. snoscan \u4e0e snoGPS \u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h1>\n<p>snoscan \u7684\u4e0b\u8f7d\u548c\u5b89\u88c5\uff1a<\/p>\n<pre>\r\n$ wget lowelab.ucsc.edu\/software\/snoscan.tar.gz\r\n$ tar zxf snoscan.tar.gz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/snoscan-0.9b\/squid-1.5j\r\n$ perl -p -i -e 's\/getline\/get_line\/g' sqio.c\r\n$ cd ..\r\n$ make\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/snoscan-0.9b' >> ~\/.bashrc\r\n$ perl -p -i -e 's#\/usr\/local\/bin\/perl#\/usr\/bin\/perl#' sort-snos\r\n<\/pre>\n<p>snoGPS \u7684\u4e0b\u8f7d\u548c\u5b89\u88c5\uff1a<\/p>\n<pre>\r\n$ wget http:\/\/lowelab.ucsc.edu\/software\/snoGPS-0.2.tar.gz\r\n$ tar zxf snoGPS-0.2.tar.gz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/snoGPS-0.2\/src\r\n$ perl -p -i -e 's\/getline\/get_line\/g' lib\/*.c squid\/lib\/*.c inc\/*.h\r\n$ make\r\n$ cd ..\r\n$ ln -s src\/pseudoU_test snoGPS\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/snoGPS-0.2' >> ~\/.bashrc \r\n$ source ~\/.bashrc\r\n$ perl -p -i -e 's#\/usr\/local\/bin\/perl#\/usr\/bin\/perl#' \/opt\/biosoft\/snoGPS-0.2\/scripts\/*.pl\r\n$ echo 'export PERL5LIB=$PERL5LIB:\/opt\/biosoft\/snoGPS-0.2\/perlModules\/' >> ~\/.bashrc\r\n$ sudo cpan -i Class::MethodMaker File::Sort Bio::Tools::Run::Alignment::TCoffee\r\n<\/pre>\n<h1>3. snoscan \u7684\u4f7f\u7528<\/h1>\n<p>snoscan\u7684\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$ snoscan rRNA.fa genome.fasta -s -o out\r\n\r\nrRNA.fa      : rRNA\u5e8f\u5217\u7684fasta\u683c\u5f0f\r\ngenome.fasta : \u7528\u4e8e\u641c\u7d22 snoRNAs \u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\r\n<\/pre>\n<p>snoscan\u7684\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-h\r\n    \u6253\u5370\u5e2e\u52a9\u4fe1\u606f\r\n-m string\r\n    \u6307\u5b9a\u5305\u542b\u7532\u57fa\u5316\u4f4d\u70b9\u4fe1\u606f\u7684\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u7684\u683c\u5f0f\u4e3a\uff1a\r\n        >seq_A\r\n        T 5 Verified meth site by TML\r\n        C 12  Predicted by snoscan\r\n        >My-seq-B\r\n        G 1   Partially modified site\r\n        A 6   Mapped by Maden\r\n    \u4e0efasta\u683c\u5f0f\u7c7b\u4f3c\uff0c\u5934\u90e8\u662f\u548c genome.fasta \u5e8f\u5217\u540d\u76f8\u540c\uff1b\u5185\u5bb9\u90e8\u5206\u52063\u5217\uff0c\u4ee5\u7a7a\u683c\u6216\u5236\u8868\u7b26\u5206\u5272\uff0c\u7b2c1\u5217\u662f\u4f4d\u70b9\u7684\u78b1\u57fa\uff0c\u7b2c2\u5217\u662f1-based\u7684\u4f4d\u70b9\uff0c\u7b2c3\u5217\u662f60\u4e2a\u5b57\u7b26\u4ee5\u5185\u7684\u63cf\u8ff0\u3002\r\n-o string\r\n    \u5c06\u7ed3\u6784\u8f93\u51fa\u5230\u6307\u5b9a\u7684\u6587\u4ef6\uff0c\u9ed8\u8ba4\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\r\n-s\r\n    \u662f\u5426\u4fdd\u5b58 snoRNA \u7684\u5e8f\u5217\u5230\u8f93\u51fa\u4e2d\r\n<\/pre>\n<h1>4. snoGPS \u7684\u4f7f\u7528<\/h1>\n<h2>4.1 \u83b7\u5f97\u53ef\u80fd\u7684\u5047\u5c3f\u82f7\u9178\u5316\u4f4d\u70b9\u5e8f\u5217<\/h2>\n<p>\u9996\u5148\uff0c\u63d0\u53d6 rRNA \u5e8f\u5217\u4fe1\u606f\u4e2d\u53ef\u80fd\u53d1\u751f\u5047\u5c3f\u82f7\u9178\u5316\u7684\u4f4d\u70b9\u3002\u4e00\u822c\u60c5\u51b5\u4e0b\uff0c\u8ba4\u4e3a\u6240\u6709\u78b1\u57fa\u4e3a U \u7684\u4f4d\u70b9\u90fd\u53ef\u80fd\u53d1\u751f\u5047\u5c3f\u82f7\u9178\u5316\u4fee\u9970\u3002\u901a\u8fc7\u7a0b\u5e8f\u5c06 \u78b1\u57faU\u53ca\u5176\u4fa7\u7ffc10bp\u5e8f\u5217\u63d0\u53d6\u51fa\u6765\uff0c\u63d0\u53d6\u51fa\u6765\uff0c\u5f97\u5230 target \u6587\u4ef6\u3002<\/p>\n<pre>\r\n$ \/opt\/biosoft\/snoGPS-0.2\/scripts\/getRnaTargets.pl -n rRNA.fa \r\n\r\n-n\r\n    \u5c06\u6240\u6709\u7684\u4f4d\u70b9\u4fe1\u606f\u5199\u5165\u5230\u4e00\u4e2a\u6587\u4ef6\u4e2d\u3002\r\n-r\r\n    \u5236\u4f5c\u53cd\u5411 RNA \u5e8f\u5217\u7684 targets\u3002\r\n-f string\r\n    \u8f93\u5165\u542b\u6709\u76ee\u6807\u5e8f\u5217\u5047\u5c3f\u82f7\u9178\u5316\u4fee\u9970\u7684\u4f4d\u70b9\u4fe1\u606f\u7684\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u683c\u5f0f\u4f8b\u5982\uff1a\r\n        rRNA1 species 43:46:53\r\n        rRNA2 species 6:7:15:34:37:39:41:43:44:54:58:60:69:72:89:91\r\n    \u6587\u4ef6\u5185\u5bb9\u4e3a\u7528\u7a7a\u683c\u5206\u5272\u76843\u5217\u3002\u7b2c1\u5217\u662frRNA\u5e8f\u5217\u540d\uff1b\u7b2c2\u5217\u662f\u4e00\u4e2a\u5355\u8bcd\u7684\u63cf\u8ff0\uff1b\u7b2c3\u5217\u662f\u5047\u5c3f\u82f7\u9178\u4f4d\u70b9\u3002    \r\n-s string\r\n    \u6bd4\u5982\u8f93\u5165 '656:989:2010'\uff0c\u5219\u5bf9\u6307\u5b9a\u4f4d\u70b9\u7684\u5c3f\u82f7\u9178\u5236\u4f5c target \u6587\u4ef6\u3002\u9ed8\u8ba4\u4e0b\u662f\u5bf9\u6240\u6709\u5c3f\u82f7\u9178\u4f4d\u70b9\u5236\u4f5c target \u6587\u4ef6\u3002\r\n<\/pre>\n<h2>4.2 \u8fd0\u884csnoGPS<\/h2>\n<p>snoGPS \u7684\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$ snoGPS -D 0 -S 15 -T snoGPS_tmp\/uridin_target_file_for_snoGPS.txt \\\r\n  -F snoGPS_hits.fa -L \/opt\/biosoft\/snoGPS-0.2\/scoretables\/haca2stemv7.tables \\\r\n  genome.fasta \/opt\/biosoft\/snoGPS-0.2\/desc\/haca2stemv4a.desc > snoGPS_out\r\n\r\ngenome.fasta : \u5728\u8be5\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e2d\u9274\u5b9a snoRNAs\u3002\r\nhaca2stemv4a.desc : \u8be5\u6587\u4ef6\u4e3a desc \u6587\u4ef6\uff0c\u7528\u4e8e\u51b3\u5b9a\u4e00\u4e9b\u53c2\u6570\u3002\u5bf9\u4e8ehuman\u548cyeast\u6709\u4e0d\u540c\u7684desc\u6587\u4ef6\u3002\r\n\u7a0b\u5e8f\u5c06\u4e3b\u8981\u7ed3\u679c\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\u3002\r\n<\/pre>\n<p>snoGPS \u7684\u5e38\u7528\u60e8\u7d20\uff1a<\/p>\n<pre>\r\n-h\r\n    \u6253\u5370\u5e2e\u52a9\u6587\u6863\r\n-S float\r\n    \u8bbe\u7f6e\u5f97\u5206\u9608\u503c\u3002\r\n-T string\r\n    \u8bbe\u7f6e target \u6587\u4ef6\uff0c\u5373\u542b\u6709\u53ef\u80fd\u7684\u5047\u5c3f\u82f7\u9178\u5316\u4fee\u9970\u4f4d\u70b9\u4fe1\u606f\u7684\u6587\u4ef6\uff0c\u7531rRNA\u5e8f\u5217\u4fe1\u606f\u83b7\u5f97\u3002\r\n-F string\r\n    \u8f93\u51fa\u7684 hits \u6587\u4ef6\u3002\u5176\u4e2d\u4e3a snoRNAs \u5e8f\u5217\u3002\r\n-t int\r\n    \u8bbe\u7f6e\u4ece target \u6587\u4ef6\u4e2d\u8bfb\u53d6\u7684 target \u4f4d\u70b9\u6570\u76ee\u3002\r\n-L string\r\n    \u8f7d\u5165 score-tables \u6587\u4ef6\u3002snoGPS \u63d0\u4f9b\u4e862\u4e2a\u6587\u4ef6\uff0c\u5206\u522b\u9002\u5408\u4e8e human \u548c yeast\u3002\u8be5\u6587\u4ef6\u4f4d\u4e8e \/opt\/biosoft\/snoGPS-0.2\/scoretables\/ \u76ee\u5f55\u4e0b\u3002\r\n-W\r\n    \u4ec5\u4ec5\u5bf9\u6b63\u94fe\u8fdb\u884c\u68c0\u6d4b\r\n-C\r\n    \u4ec5\u4ec5\u5bf9\u8d1f\u94fe\u8fdb\u884c\u68c0\u6d4b\r\n<\/pre>\n<h1>5. snoRNA \u7684\u4e00\u4e9b\u77e5\u8bc6\u70b9<\/h1>\n<p><a href=\"http:\/\/en.wikipedia.org\/wiki\/Small_nucleolar_RNA\" target=\"_blank\">Small nucleolar RNA \u7684 wikipedia<\/a>\u3002<\/p>\n<p>snoRNA \u6307\u5bfc\u7684 rRNA \u7684\u8f6c\u5f55\u540e\u4fee\u9970\u6709 2 \u79cd\uff1a \u7532\u57fa\u5316(Methylation) \u548c \u5047\u5c3f\u82f7\u9178\u5316(Pseudouridylation)\u3002<\/p>\n<p>snoRNP(small nucleolar ribonucleoprotein): \u6bcf\u4e2a snoRNA \u548c\u81f3\u5c114\u4e2a\u86cb\u767d\u5206\u5b50\u5f62\u6210\u590d\u5408\u7269\uff0c\u6765\u6307\u5bfc\u76ee\u6807RNA\u7684\u4fee\u9970\u3002<\/p>\n<p>snoRNAs \u4e3b\u8981\u6709 2 \u79cd\u4e0d\u540c\u7c7b\u578b\u3002\u5176\u4e2d C\/D box \u7c7b\u578b\u7528\u4e8e\u6307\u5bfc\u7532\u57fa\u5316\u4fee\u9970\uff1b H\/ACA box \u7c7b\u578b\u7528\u4e8e\u6307\u5bfc\u5047\u5c3f\u82f7\u9178\u5316\u4fee\u9970\u3002<\/p>\n<p>C\/D box \u7c7b\u578b\u7684 snoRNAs \u5305\u542b C(RUGAUGA)\u73af \u548c D(CUGA)\u73af\uff0c\u5206\u522b\u5728 snoRNA \u7684 5&#8242; \u548c 3&#8242; \u7aef\u3002\u5982\u4e0b\u56fe\u6240\u793a\uff1a<br \/>\n<img src=\"http:\/\/bioinf.scri.sari.ac.uk\/images\/snorna\/cd.jpg\" alt=\"C\/D box\" \/><\/p>\n<p>H\/ACA box \u7c7b\u578b\u7684 snoRNAs \u7531 2 \u4e2a\u53d1\u5939\u7ed3\u6784\u548c 2 \u4e2a\u5355\u94fe\u533a\u7ec4\u6210\uff0c\u79f0\u4e3a hairpin-hinge-hairpin-tail \u7ed3\u6784\uff0c\u5982\u4e0b\u56fe\u6240\u793a\u3002\u7ed3\u6784\u4e2d\u5305\u542b H box(ANANNA) \u548c ACA box(ACA)\u3002<br \/>\n<img src=\"http:\/\/bioinf.scri.sari.ac.uk\/images\/snorna\/haca.jpg\" alt=\"H\/ACA box\" \/><\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. snoscan \u548c snoGPS \u7b80\u4ecb snoRNAs \u4e3b\u8981\u6709 2 \u79cd\u4e0d\u540c &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2325\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[78],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2325"}],"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=2325"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2325\/revisions"}],"predecessor-version":[{"id":2326,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2325\/revisions\/2326"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2325"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2325"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2325"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}