{"id":2205,"date":"2014-07-05T22:49:12","date_gmt":"2014-07-05T14:49:12","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2205"},"modified":"2014-07-07T00:34:42","modified_gmt":"2014-07-06T16:34:42","slug":"antismash-%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2205","title":{"rendered":"antiSMASH \u4f7f\u7528"},"content":{"rendered":"

1. antiSMASH \u7b80\u4ecb<\/h1>\n

antiSMASH \u7528\u4e8e\u5bfb\u627e\u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u7c07\u3002\u4e00\u822c\u60c5\u51b5\u4e0b\uff0c\u53c2\u4e0e\u6b21\u7ea7\u4ee3\u8c22\u9014\u5f84\u4e2d\u751f\u7269\u5408\u6210\u9176\u7684\u57fa\u56e0\u5728\u67d3\u8272\u4f53\u4e0a\u6210\u7c07\u6392\u5217\u3002\u57fa\u4e8e\u6307\u5b9a\u7c7b\u578b\u7684 profile hidden Markov models\uff0c antiSMASH \u80fd\u51c6\u786e\u9274\u5b9a\u6240\u6709\u5df2\u77e5\u7684\u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u7c07\u3002
\nantiSMASH \u7684\u4f7f\u7528\u8bf4\u660e\uff1ahttp:\/\/antismash.secondarymetabolites.org\/help.html<\/a>
\nantiSMASH \u7684\u53c2\u8003\u6587\u732e\uff1aantiSMASH 2.0 \u2014 a versatile platform for genome mining of secondary metabolite producers.
\n Kai Blin, Marnix H. Medema, Daniyal Kazempour, Michael A. Fischbach, Rainer Breitling, Eriko Takano, & Tilmann Weber
\nNucleic Acids Research (2013), doi: 10.1093\/nar\/gkt449<\/a>.<\/p>\n

2. \u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u7c07\u7b80\u4ecb<\/h1>\n

\u5728 antiSMASH \u4e2d\uff0c\u5c06\u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u7c07\u5206\u4e3a\u4e86 24 \u7c7b\u3002
\n\u6700\u5e38\u89c1\u7684\u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u7c07\u662f type I, II and III polyketides synthase(PKS) \u548c non-ribosomal peptides synthase(NRPS)\u3002\u4f8b\u5982\uff1a\u56db\u73af\u7d20\u3001\u5927\u73af\u5185\u916f\u7c7b\u3001\u5b89\u838e\u7c7b\u3001\u805a\u919a\u7c7b\u7531 PKS \u9014\u5f84\u5408\u6210\uff1bbeta-\u5185\u9170\u80fa\u7c7b\u3001\u591a\u80bd\u7c7b\u3001\u7cd6\u80bd\u7c7b\u7531 NRPS \u9014\u5f84\u5408\u6210\u3002
\n\u6b64\u5916\uff0c\u8fd8\u6709 heterocyst glycolipid-like polyketides, terpenes, lantibiotics, bacteriocins, \u03b2-lactams, aminoglycosides\/aminocyclitols, aminocoumarins, siderophores, ectoines, butyrolactones, indoles, nucleosides, phosphoglycolipids, melanins, oligosaccharide, furans, homoserine lactones, thiopeptides, phenazines, others.<\/p>\n

3. antiSMASH \u5b89\u88c5<\/h1>\n

\u9996\u5148\u8981\u5b89\u88c5 ncbi-blast+, hmmer3.0, hmmer2.3.2(hmmpfam), glimmer3, GlimmerHMM 3.0.2, muscle.
\n\u5b89\u88c5 ncbi-blast+<\/p>\n

\r\n$ wget ftp:\/\/ftp.ncbi.nih.gov\/blast\/executables\/LATEST\/ncbi-blast-2.2.29+-x64-linux.tar.gz\r\n$ tar zxf ncbi-blast-2.2.29+-x64-linux.tar.gz -C \/opt\/biosoft\/\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/ncbi-blast-2.2.29+\/bin\/' >> ~\/.bashrc\r\n<\/pre>\n
\u5b89\u88c5 hmmer3.0<\/p>\n
\r\n$ wget http:\/\/selab.janelia.org\/software\/hmmer3\/3.0\/hmmer-3.0.tar.gz\r\n$ tar zxf hmmer-3.0.tar.gz\r\n$ cd hmmer-3.0\r\n$ .\/configure --prefix=\/opt\/biosoft\/hmmer-3.0\/ && make -j 4 && make install\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/hmmer-3.0\/bin\/' >> ~\/.bashrc\r\n<\/pre>\n
\u5b89\u88c5 hmmer2.3.2<\/p>\n
\r\n$ wget http:\/\/selab.janelia.org\/software\/hmmer\/2.3.2\/hmmer-2.3.2.tar.gz\r\n$ tar zxf hmmer-2.3.2.tar.gz\r\n$ cd hmmer-2.3.2\r\n$ .\/configure --prefix=\/opt\/biosoft\/hmmer-2.3.2\/ && make -j 4 && make check\r\n$ sed -e \"s#\\(cp src\/\\$\\$file \\$(BINDIR)\/\\);#\\1\\$\\${file}2;#\" -i Makefile\r\n$ make install\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/hmmer-2.3.2\/bin\/' >> ~\/.bashrc\r\n<\/pre>\n
\u5b89\u88c5 glimmer3<\/p>\n
\r\n$ wget http:\/\/ccb.jhu.edu\/software\/glimmer\/glimmer302.tar.gz\r\n$ tar zxf glimmer302.tar.gz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/glimmer3.02\r\n$ wget https:\/\/bitbucket.org\/antismash\/antismash2\/downloads\/Allow-glimmer-to-compile-on-g-4.4.3.patch -O Allow-glimmer-to-compile-on-g-4.4.3.patch\r\n$ patch -p1 < Allow-glimmer-to-compile-on-g-4.4.3.patch\r\n$ cd src\r\n$ make -j 4\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/glimmer3.02\/bin\/' >> ~\/.bashrc\r\n<\/pre>\n
\u5b89\u88c5 GlimmerHMM 3.02<\/p>\n
\r\n$ wget ftp:\/\/ccb.jhu.edu\/pub\/software\/glimmerhmm\/GlimmerHMM-3.0.2.tar.gz\r\n$ tar zxf GlimmerHMM-3.0.2.tar.gz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/GlimmerHMM\/sources\r\n$ make\r\n$ cp glimmerhmm ..\/bin\/\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/GlimmerHMM\/bin\/' >> ~\/.bashrc\r\n<\/pre>\n
\u5b89\u88c5 Muscle<\/p>\n
\r\n$ wget http:\/\/www.drive5.com\/muscle\/downloads3.8.31\/muscle3.8.31_src.tar.gz\r\n$ tar zxf muscle3.8.31_src.tar.gz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/muscle3.8.31\/src\r\n$ make -j 4\r\n$ mkdir ..\/bin\/\r\n$ cp muscle ..\/bin\/\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/muscle3.8.31\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n
\u5b89\u88c5\u4e00\u4e9b\u7cfb\u7edf\u8f6f\u4ef6\uff1a<\/p>\n
\r\n$ sudo yum install -y perl-Archive-Tar python-pip python-virtualenv git java-1.7.0-openjdk python-devel libxslt-devel libxml2-devel gcc-c++ patch glibc-static cairo\r\n$ wget http:\/\/dl.fedoraproject.org\/pub\/epel\/6\/x86_64\/epel-release-6-8.noarch.rpm\r\n$ sudo rpm -Uvh epel-release-6-8.noarch.rpm\r\n<\/pre>\n
\u5b89\u88c5 antiSMASH\u3002\u53ef\u4ee5\u4e0d\u9700\u8981\u4ee5\u4e0a\u6240\u6709\u6b65\u9aa4\uff0c\u76f4\u63a5\u8fdb\u884c\u4e0b\u9762\u7684\u5b89\u88c5\uff08\u9700\u8981\u8054\u7f51\uff09\u3002\u4ee5\u4e0a\u6b65\u9aa4\u5219\u662f\u5c06\u6240\u6709\u7684\u7a0b\u5e8f\u5b89\u88c5\u5230 \/opt\/biosoft \u76ee\u5f55\u4e0b\uff0c\u4ee5\u4fbf\u4e8e\u7ba1\u7406\u751f\u7269\u4fe1\u606f\u5b66\u8f6f\u4ef6\u3002<\/p>\n
\r\n$ mkdir \/opt\/biosoft\/antiSMASH\/\r\n$ cd \/opt\/biosoft\/antiSMASH\/\r\n$ wget https:\/\/bitbucket.org\/antismash\/antismash2\/downloads\/install_centos.sh -O install_centos.sh\r\n\u6b64\u6587\u4ef6\u4e2d\u6709\u5904\u9519\u8bef\uff0c\u5bfc\u81f4\u4e0b\u8f7d\u4e0d\u4e86 antiSMASH \u7684\u8f6f\u4ef6\u5305\u3002\r\n$ perl -p -i -e 's#\\\"\\${ANTISMASH_BASE}\\${ANTISMASH_TARBALL}\\\"#\\${ANTISMASH_BASE}\/\\${ANTISMASH_TARBALL} -O \\${ANTISMASH_BASE}#' install_centos.sh\r\n\u6b64\u811a\u672c\u9002\u5408\u4e8e CentOS 6.4 \u7cfb\u7edf\uff0c\u5982\u679c\u662f CentOS 6.5 \u7cfb\u7edf\uff0c \u5219\u8981\u591a\u8fdb\u884c\u4e0b\u4e00\u6b65\r\n$ perl -p -i -e 's\/6_4\/6_5\/' install_centos.sh\r\n$ sh install_centos.sh\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/antiSMASH\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n$ run_antismash\r\n<\/pre>\n
4. antiSMASH \u4f7f\u7528<\/h1>\n
4.1 \u6ce8\u610f\u4e8b\u9879<\/h2>\n
antiSMASH \u652f\u6301 Fasta\/Genbank\/EMBL \uff08\u8981\u5206\u522b\u4ee5 .fasta .gbk .embl \u4f5c\u4e3a\u540e\u7f00\u4ee5\u5229\u4e8e\u7a0b\u5e8f\u8bc6\u522b\uff09\u683c\u5f0f\u7684\u6587\u4ef6\u4f5c\u4e3a\u8f93\u5165\u3002\u63a8\u8350\u4f7f\u7528 Genbank \u683c\u5f0f\u6587\u4ef6\u4f5c\u4e3a\u8f93\u5165\u3002\u8be5\u6587\u4ef6\u5305\u542b\u4e86\u7f16\u7801\u86cb\u767d\u57fa\u56e0\u7684\u6ce8\u91ca\u4fe1\u606f\u3002\u5426\u5219\uff0c\u4ee5 fasta \u6587\u4ef6\u4f5c\u4e3a\u8f93\u5165\uff0c\u7a0b\u5e8f\u5219\u9700\u8981\u8c03\u7528 Glimmer3 \u548c GlimmerHMM \u6765\u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\u540e\u518d\u8fdb\u884c\u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u7c07\u7684\u9274\u5b9a\u3002
\n\u4f7f\u7528 –clusterblast \u548c –subclusterblast \u53c2\u6570\uff0cantiSMASH \u4f7f\u7528 blastp \u6765\u5c06\u6c28\u57fa\u9178\u5e8f\u5217\u6bd4\u5bf9\u5230\u5df2\u77e5\u7684\u6b21\u7ea7\u4ee3\u8c22 clusters \u6216 subclusters \u4e0a\uff0c\u6765\u5bfb\u627e query \u5e8f\u5217\u4e2d\u7684\u57fa\u56e0\u7c07\u3002\u7f51\u9875\u7248\u4e2d\u9ed8\u8ba4\u4f7f\u7528\u6b64\u53c2\u6570\u3002
\n\u4f7f\u7528 –smcogs \u53c2\u6570\uff0cantiSMASH \u80fd\u5206\u6790\u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u5bb6\u65cf \uff08smCOGs\uff09\uff0c\u5e76\u4f7f\u7528\u5176\u5bb6\u65cf\u7684\u57fa\u56e0\uff08\u6700\u591a100\u4e2a\uff09\u6784\u5efa\u7cfb\u7edf\u53d1\u80b2\u6811\u3002\u7f51\u9875\u7248\u4e2d\u9ed8\u8ba4\u4f7f\u7528\u6b64\u53c2\u6570\u3002
\n\u4f7f\u7528 –full-hmmer \u53c2\u6570\uff0c antiSMASH \u5c06\u8fdb\u884c\u5168\u57fa\u56e0\u7ec4\u7684 PFAM \u5206\u6790\uff0c\u5bfb\u627e\u6b21\u7ea7\u4ee3\u8c22 domains \u51fa\u73b0\u8fc7\u4e8e\u9891\u7e41\u7684\u57fa\u56e0\u7ec4\u533a\u57df\u3002\u8fd9\u6837\u80fd\u627e\u5230\u4e00\u4e9b clusterblast \u6b65\u9aa4\u4e2d\u6f0f\u6389\u7684\u57fa\u56e0\u7c07\u3002\u7f51\u9875\u7248\u4e2d\u9ed8\u8ba4\u4f7f\u7528\u6b64\u53c2\u6570\u3002<\/p>\n
4.2 \u5e38\u7528\u4f8b\u5b50<\/h2>\n
\r\n$ run_antismash --clusterblast --subclusterblast --smcogs --full-hmmer species.gbk\r\n<\/pre>\n
\u7ed3\u679c\u6587\u4ef6\u751f\u6210\u4e8e species \u6587\u4ef6\u5939\u4e0b\u3002\u70b9\u51fb index.html \u8fdb\u884c\u7ed3\u679c\u7684\u7f51\u9875\u67e5\u770b\u3002
\n\u6709\u5173\u4e8e\u57fa\u56e0\u7ec4 genbank \u6587\u4ef6\u7684\u751f\u6210\uff0c\u53ef\u4ee5\u4f7f\u7528 tbl2asn \u8f6f\u4ef6\u8fdb\u884c\u751f\u6210\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
1. antiSMASH \u7b80\u4ecb antiSMASH \u7528\u4e8e\u5bfb\u627e\u6b21\u7ea7\u4ee3\u8c22\u57fa\u56e0\u7c07\u3002\u4e00\u822c … \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\/2205"}],"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=2205"}],"version-history":[{"count":7,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2205\/revisions"}],"predecessor-version":[{"id":2212,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2205\/revisions\/2212"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2205"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2205"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2205"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}