{"id":1376,"date":"2013-06-03T18:13:19","date_gmt":"2013-06-03T10:13:19","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1376"},"modified":"2013-06-04T16:16:49","modified_gmt":"2013-06-04T08:16:49","slug":"cazyme%e6%b3%a8%e9%87%8a","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1376","title":{"rendered":"CAZyme\u6ce8\u91ca\u6b65\u9aa4"},"content":{"rendered":"<p>CAZyme\u7684\u6570\u636e\u6765\u6e90\u4e8eCAZyDB\uff1a<a href=\"http:\/\/www.cazy.org\" target=\"_blank\">www.cazy.org<\/a>;\u800c\u5bf9CAZyme\u7684\u6ce8\u91ca\u4e3b\u8981\u4f7f\u7528dbCAN\uff1a<a href=\"http:\/\/csbl.bmb.uga.edu\/dbCAN\/index.php\" target=\"_blank\">http:\/\/csbl.bmb.uga.edu\/dbCAN\/<\/a>\u3002\u5bf9CAZyme\u7684\u6ce8\u91ca\u6b65\u9aa4\u5982\u4e0b\uff1a<\/p>\n<h2>1. \u4ecedbCAN\u4e2d\u4e0b\u8f7dHMMs<\/h2>\n<p>\u6253\u5f00dbCAN\u7f51\u7ad9\u7684<a href=\"http:\/\/csbl.bmb.uga.edu\/dbCAN\/download.php\" target=\"_blank\">Download\u9875\u9762<\/a>\u3002\u4e0b\u8f7d\u5176\u4e2d\u76843\u4e2a\u6587\u4ef6\uff1aall.hmm.ps.len\uff0cdbCAN-fam-HMMs.txt\uff0chmmscan-parser.sh\u3002<\/p>\n<h2>2. \u4e0b\u8f7dhmmer\u8f6f\u4ef6<\/h2>\n<p>\u4ece<a href=\"http:\/\/hmmer.org\/\" target=\"_blank\">http:\/\/hmmer.org\/<\/a>\u4e0b\u8f7d<a href=\"ftp:\/\/selab.janelia.org\/pub\/software\/hmmer3\/3.0rc2\/hmmer-3.0rc2.tar.gz\" target=\"_blank\">hmmer3.0rc2<\/a>\u5e76\u5b89\u88c5\u3002<\/p>\n<h2>3. \u5bf9\u76ee\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u8fdb\u884c\u6ce8\u91ca<\/h2>\n<p>\u76ee\u7684\u86cb\u767d\u8d28\u5e8f\u5217\u5e38\u5e38\u662f\u5168\u57fa\u56e0\u7ec4\u7684\u9884\u6d4b\u86cb\u767d\u3002\u6bd4\u5982\u5176\u6587\u4ef6\u540d\u4e3aspecies_protein.fasta.CAZyme\u6ce8\u91ca\u8fc7\u7a0b\u4e3a\uff1a<\/p>\n<pre>\r\n$ hmmpress dbCAN-fam-HMMs.txt\r\n$ hmmscan dbCAN-fam-HMMs.txt species_protein.fasta > CAZyme_species.dbCAN\r\n$ sh hmmscan-parser.sh CAZyme_species.dbCAN > CAZyme_species.annot\r\n<\/pre>\n<p>\u7a0b\u5e8f\u5f88\u5feb\u8fd0\u884c\u5b8c\u6bd5\uff0cCAZyme\u7684\u6ce8\u91ca\u7ed3\u679c\u6587\u4ef6\u4e3aCAZyme_species.annot\u3002<\/p>\n<h2>4. \u7ed3\u679c\u6587\u4ef6<\/h2>\n<p>CAZyme_species.annot\u7684\u6587\u4ef6\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n<pre>scaffold_1.30   GH28.hmm        1.5e-58 9       308     60      361     0.92\r\nscaffold_1.30.1 GH28.hmm        1.5e-58 9       308     60      361     0.92\r\nscaffold_1.90   GT32.hmm        1.2e-23 2       87      81      161     0.944444444444444\r\nscaffold_1.94   GH18.hmm        3.5e-64 5       288     127     486     0.956081081081081\r\nscaffold_10.18  GH105.hmm       1.1e-84 14      332     49      392     0.957831325301205\r\nscaffold_10.20  CBM1.hmm        9.1e-14 1       29      26      54      0.96551724137931\r\nscaffold_100.3  GT15.hmm        4.5e-126        1       272     75      345     0.992673992673993\r\nscaffold_100.3.1        GT15.hmm        5.4e-105        1       240     75      313     0.875457875457875\r\nscaffold_100.4  GT15.hmm        1.4e-128        1       272     70      340     0.992673992673993\r\n<\/pre>\n<p>\u6bcf\u4e00\u5217\u7684\u63cf\u8ff0\u4e3a\uff1a\u86cb\u767d\u8d28\u5e8f\u5217\u540d\u79f0\uff0c\u6240\u5c5e\u5bb6\u65cf\uff0cE-value\uff0chmm\u6a21\u578b\u5339\u914d\u8d77\u59cb\uff0chmm\u6a21\u578b\u7684\u5339\u914d\u7ed3\u675f\uff0c\u67e5\u8be2\u5e8f\u5217\u8d77\u59cb\uff0c\u67e5\u8be2\u5e8f\u5217\u7ed3\u675f\uff0c\u8986\u76d6\u5ea6\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>CAZyme\u7684\u6570\u636e\u6765\u6e90\u4e8eCAZyDB\uff1awww.cazy.org;\u800c\u5bf9CAZyme &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1376\">\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":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1376"}],"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=1376"}],"version-history":[{"count":12,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1376\/revisions"}],"predecessor-version":[{"id":1388,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1376\/revisions\/1388"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1376"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1376"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1376"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}