{"id":2746,"date":"2019-04-08T23:48:33","date_gmt":"2019-04-08T15:48:33","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2746"},"modified":"2019-04-09T00:35:12","modified_gmt":"2019-04-08T16:35:12","slug":"%e4%bd%bf%e7%94%a8signalp%e5%af%b9%e8%9b%8b%e7%99%bd%e5%ba%8f%e5%88%97%e8%bf%9b%e8%a1%8c%e4%bf%a1%e5%8f%b7%e8%82%bd%e9%a2%84%e6%b5%8b","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2746","title":{"rendered":"\u4f7f\u7528SignalP\u5bf9\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u4fe1\u53f7\u80bd\u9884\u6d4b"},"content":{"rendered":"\n

1. \u4fe1\u53f7\u80bd\u7b80\u4ecb<\/a><\/h2>\n\n\n\n

\u4fe1\u53f7\u80bd\u662f\u86cb\u767d\u8d28N-\u672b\u7aef\u4e00\u6bb5\u7f16\u7801\u957f\u5ea6\u4e3a5-30\u7684\u758f\u6c34\u6027\u6c28\u57fa\u9178\u5e8f\u5217\uff0c\u7528\u4e8e\u5f15\u5bfc\u65b0\u5408\u6210\u86cb\u767d\u8d28\u5411\u901a\u8def\u8f6c\u79fb\u7684\u77ed\u80bd\u94fe\u3002\u4fe1\u53f7\u80bd\u5b58\u5728\u4e8e\u5206\u6ccc\u86cb\u767d\u3001\u8de8\u819c\u86cb\u767d\u548c\u771f\u6838\u751f\u7269\u7ec6\u80de\u5668\u5185\u7684\u86cb\u767d\u4e2d\u3002<\/p>\n\n\n\n

\u4fe1\u53f7\u80bd\u6307\u5f15\u86cb\u767d\u8d28\u8f6c\u79fb\u7684\u65b9\u5f0f\u6709\u4e24\u79cd\uff1a\uff081\uff09\u5e38\u89c4\u7684\u5206\u6ccc\uff08Sec\/secretory\uff09\u901a\u8def\uff1b\uff082\uff09\u53cc\u7cbe\u6c28\u9178\u8f6c\u79fb\uff08Tat\/twin-arginine\uff09\u901a\u8def\u3002\u524d\u8005\u5b58\u5728\u4e8e\u539f\u6838\u751f\u7269\u86cb\u767d\u8d28\u8f6c\u79fb\u5230\u8d28\u819c\u8fc7\u7a0b\u4e2d\uff0c\u4ee5\u53ca\u771f\u6838\u751f\u7269\u86cb\u767d\u8d28\u8f6c\u79fb\u5230\u5185\u8d28\u7f51\u819c\u7684\u8fc7\u7a0b\u4e2d\u3002\u540e\u8005\u5b58\u5728\u4e8e\u7ec6\u83cc\u3001\u53e4\u83cc\u3001\u53f6\u7eff\u4f53\u548c\u7ebf\u7c92\u4f53\u4e2d\uff0c\u4fe1\u53f7\u80bd\u5e8f\u5217\u8f83\u957f\u3001\u758f\u6c34\u6027\u8f83\u5f31\u4e14\u5c3e\u90e8\u533a\u542b\u6709\u4e24\u4e2a\u8fde\u7eed\u7cbe\u6c28\u9178\u3002\u76f8\u6bd4\u4e8e\u524d\u8005\u8f6c\u8fd0\u975e\u6298\u53e0\u86cb\u767d\u8d28\uff0c\u540e\u8005\u80fd\u8f6c\u8fd0\u6298\u53e0\u86cb\u767d\u8d28\u8de8\u8d8a\u53cc\u5c42\u8102\u8d28\u819c \u3002<\/p>\n\n\n\n

\u4fe1\u53f7\u80bd\u6307\u5f15\u86cb\u767d\u8d28\u8f6c\u8fd0\u540e\uff0c\u5c06\u7531\u4fe1\u53f7\u80bd\u9176\u8fdb\u884c\u5207\u9664\u3002\u4fe1\u53f7\u80bd\u9176\u6709\u4e09\u79cd\uff1a\uff081\uff09\u4e00\u578b\u4fe1\u53f7\u80bd\u9176\uff08SPaseI\uff09\uff1b\uff082\uff09\u4e8c\u578b\u4fe1\u53f7\u80bd\u9176\uff08SPaseII\uff09\uff1b\uff083\uff09\u4e09\u578b\u4fe1\u53f7\u80bd\u9176\uff08SPaseIII\uff09\u3002\u5927\u90e8\u5206\u4fe1\u53f7\u80bd\u7531SPaseI\u8fdb\u884c\u79fb\u9664\uff0cSPaseI\u5b58\u5728\u53e4\u83cc\u3001\u7ec6\u83cc\u548c\u771f\u6838\u751f\u7269\u4e2d\uff0c\u4e14\u5728\u771f\u6838\u751f\u7269\u7684\u5185\u8d28\u7f51\u819c\u4e0a\u4ec5\u5b58\u5728\u4e00\u578b\u4fe1\u53f7\u80bd\u9176\u3002\u7ec6\u83cc\u548c\u53e4\u83cc\u8102\u86cb\u767d\u7684\u4fe1\u53f7\u80bdC\u7aef\u542b\u6709\u4e00\u6bb5\u79f0\u4e3a lipobox \u7684\u4fdd\u5b88\u533a\u57df\uff0c\u7531SPaseII\u5207\u9664\u5176\u4fe1\u53f7\u80bd\uff0c\u4e14lipobox\u7d27\u90bb\u5207\u9664\u4f4d\u70b9\uff08CS\/Cleavage Site\uff09\u7684\u6c28\u57fa\u9178\u662f\u534a\u80f1\u6c28\u9178\uff0c\u8fd9\u548c\u951a\u5b9a\u5230\u819c\u7684\u529f\u80fd\u662f\u76f8\u5173\u7684\u3002\u7ec6\u83cc\u7684\u56db\u578b\u83cc\u6bdb\u86cb\u767d\u4fe1\u53f7\u80bd\u7531SPaseIII\u8fdb\u884c\u5207\u9664\u3002\u6b64\u5916\uff1a\u5206\u6ccc\u901a\u8def\uff08Sec\uff09\u76f8\u5173\u4fe1\u53f7\u80bd\u80fd\u7531SPaseI\u3001SPaseII\u548cSPaseIII\u5207\u9664\uff0c\u4f46\u662f\u53cc\u7cbe\u6c28\u9178\u8f6c\u79fb\uff08Tat\uff09\u901a\u8def\u76f8\u5173\u4fe1\u53f7\u80bd\u4ec5\u7531 SPaseI\u548cSPaseII\u5207\u9664\u3002<\/p>\n\n\n\n

\u4f7f\u7528SignalP 5.0\u80fd\u5bf9\u539f\u6838\u751f\u7269\u7684\u4fe1\u53f7\u80bdSec\/SPI\u3001Sec\/SPII\u548cTat\/SPI\uff0c\u548c\u5bf9\u771f\u6838\u751f\u7269\u4ec5\u542b\u6709 Sec\/SPI\u4fe1\u53f7\u80bd\u8fdb\u884c\u9884\u6d4b \u3002 SignalP 5.0\u76ee\u524d\u4e0d\u80fd\u5bf9Tat\/SPII\u8fdb\u884c\u9884\u6d4b\u3002\u6b64\u5916\uff0c\u7531\u4e8e\u6ca1\u6709\u8db3\u591f\u5927\u7684\u6570\u636e\u8fdb\u884c\u8bad\u7ec3\uff0cSignalP 5.0 \u4e5f\u4e0d\u80fd\u5bf9Sec\/SPIII\u8fdb\u884c\u5206\u6790\u3002<\/p>\n\n\n\n

SignalP\u662f\u6700\u4e3a\u5e38\u7528\u7684\u4fe1\u53f7\u80bd\u5206\u6790\u8f6f\u4ef6\uff0c\u5e38\u7528\u4e8e\u5206\u6ccc\u86cb\u767d\u9884\u6d4b\u7684\u7b2c\u4e00\u6b65\u3002\u5230\u76ee\u524d2019\u5e744\u6708\uff0cSignalP\u7248\u672c\u5230\u4e86\u7b2c5\u7248\u3002\u7b2c\u4e00\u7248\u672c\u57fa\u4e8e\u4eba\u5de5\u795e\u7ecf\u7f51\u7edc\uff08Artificial Neural Network\uff09\uff1b\u7b2c\u4e8c\u7248\u672c\u5f15\u5165\u9690\u9a6c\u5c14\u79d1\u592b\u6a21\u578b\uff08Hidden Markov Models\uff09\uff1b\u7b2c\u4e09\u7248\u672c\u6539\u8fdb\u5207\u9664\u4f4d\u70b9\uff08Cleavage site\uff09\u9884\u6d4b\u65b9\u6cd5\uff1b\u7b2c\u56db\u7248\u672c\u6539\u8fdb\u5bf9\u4fe1\u53f7\u80bd\u548c\u8de8\u819c\u87ba\u65cb\u7684\u533a\u5206\u80fd\u529b\u3002\u8fd9\u56db\u4e2a\u7248\u672c\u4ec5\u80fd\u5bf9Sec\/SPI\u7c7b\u578b\u7684\u4fe1\u53f7\u80bd\u8fdb\u884c\u9884\u6d4b\u3002\u800c\u7b2c\u4e94\u7248\u672c\u7ed3\u5408\u4e86\u6df1\u5ea6\u795e\u7ecf\u7f51\u7edc\uff08deep neural network\uff09\u3001\u6761\u4ef6\u968f\u673a\u5206\u7c7b\uff08Conditional random field classification\uff09\u548c\u8fc1\u79fb\u5b66\u4e60\uff08transfer learning\uff09\u65b9\u6cd5\uff0c\u80fd\u5bf9\u4fe1\u53f7\u80bd\u8fdb\u884c\u66f4\u51c6\u786e\u7684\u9884\u6d4b\u3002<\/p>\n\n\n\n

\u53ef\u4ee5\u4f7f\u7528SignalP\u7f51\u9875\u5de5\u5177<\/a>\u8fdb\u884c\u5206\u6790\u3002\u4f46\u4e00\u6b21\u4ec5\u652f\u6301\u6700\u591a5000\u6761\u5e8f\u5217\u3002\u4ee5\u4e0b\u8bb2\u89e3\u672c\u5730\u5316\u8fd0\u884cSignalP\u8f6f\u4ef6\u3002<\/p>\n\n\n\n

2. SignalP\u8f6f\u4ef6\u4e0b\u8f7d<\/a>\u548c\u5b89\u88c5<\/h2>\n\n\n\n
# \u9700\u8981\u586b\u5199edu\u90ae\u7bb1\u548c\u76f8\u5173\u4fe1\u606f\u6765\u83b7\u53d6\u4e0b\u8f7d\u5730\u5740\n$ wget http:\/\/www.cbs.dtu.dk\/download\/6B91F6BC-5A05-11E9-8172-2ED6B9CD16B5\/signalp-5.0.Linux.tar.gz -P ~\/software\/\n$ tar zxf \/home\/train\/software\/signalp-5.0.Linux.tar.gz -C \/opt\/biosoft\/\n$ echo 'PATH=$PATH:\/opt\/biosoft\/signalp-5.0\/bin' >> ~\/.bashrc\n$ source ~\/.bashrc<\/code><\/pre>\n\n\n\n
3. SignalP\u8f6f\u4ef6\u4f7f\u7528<\/h2>\n\n\n\n
\u5bf9\u771f\u6838\u751f\u7269\u7684\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u4fe1\u53f7\u80bd\u9884\u6d4b\uff1a
$ signalp -batch 30000 -org euk -fasta proteins.fasta -gff3 -mature<\/pre>\n\n\n\n
signalp\u547d\u4ee4\u7684\u53c2\u6570\uff1a<\/strong>

<\/strong>-batch <int>    default: 10000
    \u7a0b\u5e8f\u5e76\u884c\u5316\u8fd0\u884c\u7684\u5e8f\u5217\u6761\u6570\u3002\u7a0b\u5e8f\u80fd\u591a\u7ebf\u7a0b\u8fd0\u884c\uff0c\u901f\u5ea6\u5f88\u5feb\u3002\u63a8\u8350\u8bbe\u7f6e\u8be5\u53c2\u6570\u503c\u5927\u4e8eFASTA\u6587\u4ef6\u7684\u5e8f\u5217\u603b\u6761\u6570\uff0c\u867d\u7136\u589e\u52a0\u5185\u5b58\u6d88\u8017\uff0c\u4f46\u80fd\u52a0\u5feb\u7a0b\u5e8f\u8fd0\u884c\u3002
-org <string>    default: euk
    \u8bbe\u7f6e\u5206\u6790\u7684\u7269\u79cd\u7c7b\u578b\u3002\u8be5\u53c2\u6570\u503c\u67094\u79cd\uff1aarch\uff0c\u53e4\u83cc\uff1bgram+\uff0c\u9769\u5170\u6c0f\u9633\u6027\u7ec6\u83cc\uff0cgram-\uff0c\u9769\u5170\u6c0f\u9634\u6027\u7ec6\u83cc\uff1beuk\uff0c\u771f\u6838\u751f\u7269\u3002
-fasta <string>
    \u8f93\u5165FASTA\u683c\u5f0f\u7684\u86cb\u767d\u5e8f\u5217\u6587\u4ef6\u3002
-prefix <string>
    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u524d\u7f00\u3002\u9ed8\u8ba4\u5728\u7a0b\u5e8f\u8fd0\u884c\u76ee\u5f55\u4e0b\u8f93\u51fa\u7ed3\u679c\u6587\u4ef6\uff0c\u548c\u8f93\u5165\u6587\u4ef6\u540d\u7684\u524d\u7f00\u76f8\u540c\uff0c\u540e\u7f00\u4e3a_summary.signalp5\u3002
-gff3
    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u8f93\u51faGFF3\u683c\u5f0f\u7684\u4fe1\u53f7\u80bd\u9884\u6d4b\u7ed3\u679c\u3002
-mature
    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u5bf9\u542b\u6709\u4fe1\u53f7\u80bd\u7684\u86cb\u767d\u5e8f\u5217\uff0c\u5207\u9664\u4fe1\u53f7\u80bd\u540e\u8f93\u51fa\u5176\u6210\u719f\u86cb\u767d\u5e8f\u5217\u3002\u53ef\u4ee5\u7528\u4e8e\u4e0b\u6e38\u7684\u8de8\u819c\u533a\u5206\u6790\u3002
-tmp <string>    default: \/tmp
    \u8bbe\u7f6e\u4e34\u65f6\u6587\u4ef6\u5939\u8def\u5f84\u3002
-format <string>    default: short
    \u8bbe\u7f6e\u8f93\u51fa\u683c\u5f0f\u3002\u8be5\u53c2\u6570\u503c\u6709\u4e24\u4e2a\uff1ashort\uff0c\u4ec5\u8f93\u51fa\u4e00\u4e2a\u4fe1\u53f7\u80bd\u9884\u6d4b\u7684\u6574\u5408\u6587\u672c\u7ed3\u679c\uff1blong\uff0c\u989d\u5916\u8f93\u51fa\u6bcf\u6761\u5e8f\u5217\u7684\u5404\u4f4d\u70b9\u9884\u6d4b\u6587\u672c\u7ed3\u679c\u548c\u56fe\u7247\u7ed3\u679c\uff1b 
-plot <string>    default: png
    \u8bbe\u7f6e\u8f93\u51fa\u56fe\u7247\u7ed3\u679c\u7684\u7c7b\u578b\u3002\u5f53--format\u53c2\u6570\u4e3along\u65f6\uff0c\u8be5\u53c2\u6570\u751f\u6548\u3002\u8be5\u53c2\u6570\u503c\u6709\u4e09\u4e2a\uff1apng\uff1beps\uff1bnone\u8868\u793a\u4ec5\u5f97\u5230\u8868\u683c\u6587\u4ef6\u3002
-version
    \u6253\u5370\u7a0b\u5e8f\u7248\u672c\u5e76\u9000\u51fa\u3002
<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. \u4fe1\u53f7\u80bd\u7b80\u4ecb \u4fe1\u53f7\u80bd\u662f\u86cb\u767d\u8d28N-\u672b\u7aef\u4e00\u6bb5\u7f16\u7801\u957f\u5ea6\u4e3a5-30\u7684\u758f\u6c34\u6027\u6c28\u57fa\u9178\u5e8f\u5217 … \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\/2746"}],"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=2746"}],"version-history":[{"count":7,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2746\/revisions"}],"predecessor-version":[{"id":2753,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2746\/revisions\/2753"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2746"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2746"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2746"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}