{"id":2171,"date":"2014-06-25T23:25:52","date_gmt":"2014-06-25T15:25:52","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2171"},"modified":"2014-07-11T18:36:02","modified_gmt":"2014-07-11T10:36:02","slug":"%e4%b8%8a%e4%bc%a0%e5%9f%ba%e5%9b%a0%e7%bb%84%e6%95%b0%e6%8d%ae%e5%88%b0ncbi","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2171","title":{"rendered":"\u4e0a\u4f20\u57fa\u56e0\u7ec4\u6570\u636e\u5230NCBI"},"content":{"rendered":"

\u521b\u5efa BioProject \u53f7\u548c BioSample \u53f7<\/h1>\n

\u5bf9\u67d0\u4e00\u4e2a\u7269\u79cd\u8fdb\u884c\u4e86\u57fa\u56e0\u7ec4\u6d4b\u5e8f\uff0c\u5219\u7533\u8bf7 BioProject \u548c BioSample \u53f7\u5404\u4e00\u4e2a\u3002<\/p>\n

\u4f7f\u7528 tbl2asn \u51c6\u5907\u540e\u7f00\u4e3a .sqn \u7684 ASN.1 \u6587\u4ef6<\/h1>\n

\u5728 windows \u4e0b\u53ef\u4ee5\u4f7f\u7528 Sequin<\/a> \u6765\u5236\u4f5c .sqn \u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u662f\u4e0b\u9762\u6240\u8ff0\u7684 3 \u4e2a\u6587\u4ef6\u7684\u4fe1\u606f\u7684\u7efc\u5408\u4f53\u3002tbl2asn \u662f\u547d\u4ee4\u884c\u7684\u5de5\u5177\uff0c\u9002\u5408\u5927\u57fa\u56e0\u7ec4\u6570\u636e\u7684 .sqn \u6587\u4ef6\u751f\u6210\u3002<\/p>\n

1. \u751f\u6210\u5305\u542b\u4f5c\u8005\u4fe1\u606f\u7684 .sbt \u6a21\u677f\u6587\u4ef6(Submission Template)<\/h2>\n

\u63a8\u8350\u4f7f\u7528\u7f51\u9875http:\/\/www.ncbi.nlm.nih.gov\/WebSub\/template.cgi<\/a>\uff0c\u586b\u5165\u6570\u636e\u751f\u6210 template.sbt \u6587\u4ef6\uff0c\u5e76\u4e0b\u8f7d\u5230\u672c\u5730\u3002\u5f53\u7136\uff0c\u6b64\u6587\u4ef6\u4e5f\u53ef\u4ee5\u4f7f\u7528 Sequin<\/a> \u751f\u6210\u3002
\n\u586b\u5199\u4fe1\u606f\u65f6\uff0c\u53ef\u586b\u5165 BioProject \u548c BioSample \u53f7\u3002<\/p>\n

2. \u51c6\u5907\u540e\u7f00\u4e3a .fsa \u7684fasta\u6587\u4ef6<\/h2>\n

fasta \u6587\u4ef6\u7684\u7684 header \u8981\u6c42\u5982\u4e0b\uff1a<\/p>\n

\r\n1. \">\" \u548c \u7b2c\u4e00\u4e2a\u7a7a\u683c\u4e4b\u95f4\u7684\u5185\u5bb9\u662f\u5e8f\u5217\u540d\u3002\r\n2. header\u90e8\u5206\u53ef\u4ee5\u52a0\u5165\u5176\u5b83\u56e0\u7d20\uff0c\u6bd4\u5982\uff1a\r\norganism [organism=Saccharomyces cerevisiae]\r\nstrain [strain=S288C]\r\nisolate [isolate=CWS1]  # \u4ee3\u8868\u5728\u4ec0\u4e48\u4e2a\u4f53\u4e0a\u83b7\u5f97\u7684\u6837\u54c1\r\nchromosome [chromosome=XVI]\r\ntopology [topology=circular]\r\nlocation [location=mitochondrion]\r\nmolecule [moltype=mRNA] (DNA is the default)\r\ntechnique [tech=wgs]\r\nprotein name [protein=helicase]\r\ngenetic code [gcode=4]\r\n<\/pre>\n
3. \u51c6\u5907\u540e\u7f00\u4e3a .tbl \u7684\u8868\u683c\u683c\u5f0f\u7684\u57fa\u56e0\u7ec4\u6ce8\u91ca\u4fe1\u606f\u6587\u4ef6<\/h2>\n
\u6b64\u6587\u4ef6\u6709 5 \u5217\uff0c\u6bcf\u5217\u7528 tab \u5206\u5272\uff0c\u79f0\u4e3a feature table<\/a>\u3002
\n\u6b64\u6587\u4ef6\u662f\u6700\u4e3a\u5173\u952e\u7684\u4e00\u6b65\u3002\u8be5\u6587\u4ef6\u5fc5\u987b\u5305\u542b\uff1a\u7f16\u7801\u57fa\u56e0\u7684\u7ed3\u6784\u6ce8\u91ca\u4fe1\u606f\u3001\u975e\u7f16\u7801\u57fa\u56e0\u7684\u7ed3\u6784\u6ce8\u91ca\u4fe1\u606f \u548c \u57fa\u56e0\u7684\u529f\u80fd\u6ce8\u91ca\u4fe1\u606f\u3002\u4e00\u65e6\u505a\u4e0d\u597d\uff0cNCBI\u7684\u5de5\u4f5c\u4eba\u5458\u5c31\u4f1a\u53d1email\u53cd\u9988\u4fee\u6539\u610f\u89c1\u3002<\/p>\n
feature table \u683c\u5f0f\u7684\u8981\u70b9\u5982\u4e0b\uff1a<\/p>\n
\r\n1. \u5bf9\u6bcf\u6761\u5e8f\u5217\u7684\u6240\u6709\u6ce8\u91ca\u4e4b\u524d\uff0c\u6709\u4e00\u884c\u989d\u5916\u7684\u5185\u5bb9\uff0c\u4f8b\u5982\uff1a\r\n>Feature scaffold_1\r\n\u8be5\u884c\u5185\u5bb9\u540e\u9762\u7684\u6240\u6709\u6ce8\u91ca\u4fe1\u606f\u5c5e\u4e8e\u5e8f\u5217 scaffold_1 \uff0c\u4e00\u5b9a\u4e0d\u80fd\u9057\u6f0f Feature \u8fd9\u4e2a\u5355\u8bcd\uff0cFeature \u548c scaffold_1 \u7528\u7a7a\u683c\u5206\u9694\u3002\r\n2. \u6bcf\u4e2a feature \u4f7f\u7528 5 \u884c\u5185\u5bb9\u8fdb\u884c\u9610\u8ff0\uff0c\u5e76\u5206\u6210 2 \u4e2a\u90e8\u5206\u3002\r\n\u7b2c 1 \u90e8\u5206\u662f feature \u5728\u5e8f\u5217\u4e0a\u7684\u7ed3\u6784\u4fe1\u606f\u3002\u6709 3 \u5217\uff0c\u5206\u522b\u4e3a\u8be5 feature \u7684\u8d77\u59cb\u4f4d\u70b9\u3001\u7ed3\u675f\u4f4d\u70b9\u548c feature \u540d\u3002\u82e5 feature \u5728\u6b63\u4e49\u94fe\u4e0a\uff0c\u5219\u8d77\u59cb\u4f4d\u70b9 < \u7ed3\u675f\u4f4d\u70b9\uff0c\u82e5\u5728\u8d1f\u4e49\u94fe\u4e0a\uff0c\u5219\u8d77\u59cb\u4f4d\u70b9 > \u7ed3\u675f\u4f4d\u70b9\u3002\u82e5 feature \u4e3a\u65ad\u88c2\u57fa\u56e0\u7684 CDS \u6216 exon \u7b49\u4fe1\u606f\u65f6\uff0c\u5219\u6709\u591a\u884c\u6570\u636e\uff0c\u4f46\u4ec5\u5728\u5176\u9996\u884c\u7684\u7b2c 3 \u5217\u4e0a\u663e\u793a feature \u540d\u3002\r\n\u7b2c 2 \u90e8\u5206\u662f feature \u7684\u529f\u80fd\u6ce8\u91ca\u4fe1\u606f\u3002\u4f7f\u7528\u7b2c 4\u30015 \u5217\uff0c\u524d\u9762\u6709 3 \u4e2a tab \u952e\u3002\u7b2c 4 \u5217\u5bf9\u5e94 feature \u7684 qualifier\uff0c\u7b2c 5 \u5217\u662f qualifier \u7684\u503c\u3002 qualifier \u662f\u5bf9 feature \u7684\u63cf\u8ff0\u6807\u7b7e\u3002\u5982\u679c\u6709\u591a\u4e2a qualifier \u53ca\u5176\u503c\uff0c\u5219\u7528\u591a\u884c\u8fdb\u884c\u8868\u793a\u3002\r\n3. feature \u548c qualifier \u7684\u5177\u4f53\u6807\u7b7e\u540d\u79f0\u53c2\u8003http:\/\/www.insdc.org\/documents\/feature_table.html<\/a>\u3002\r\n4. \u5e38\u7528\u7684 feature \u540d\u79f0\u6709\uff1agene, mRNA, CDS, exon, 5'UTR, 3'UTR, tRNA, rRNA, ncRNA \u7b49\u3002\u5176\u4e2d ncRNA \u662f\u6307\u9664\u4e86 tRNA \u548c rRNA \u4ee5\u5916\u7684\u5176\u4f59 ncRNA\u3002\r\n5. gene \u7684 qualifier \u6807\u7b7e\u4e00\u822c\u662f gene, \u7b2c 5 \u5217\u4f7f\u7528 NCBI \u63d0\u4f9b\u7684 locus_tag + \u6570\u5b57\u7f16\u53f7\u3002 mRNA \u548c CDS \u7684 qualifier \u6807\u7b7e\u4e00\u822c\u4f7f\u7528 product\uff0c\u7b2c 5 \u5217\u662f Nr \u6ce8\u91ca\u7684\u7ed3\u679c\u3002exon \u7684 qualifier \u6807\u7b7e\u4e00\u822c\u4f7f\u7528 number\uff0c\u5176\u503c\u4e3a 1,2,3... \u3002 UTR \u7684 qualifier \u6807\u7b7e\u53ef\u4ee5\u4f7f\u7528 note\u3002 tRNA \u7684 qualifier \u6807\u7b7e\u4e00\u822c\u4f7f\u7528 product\uff0c\u7b2c 5 \u5217\u662f tRNA \u540d\u79f0, \u4f8b\u5982 tRNA-Lys\u3002rRNA \u7684 qualifier \u6807\u7b7e\u8981\u6709 gene \u548c product\uff0c\u7b2c 5 \u5217\u4e2dproduct \u662f \"16S ribosomal RNA\", \"23S ribosomal RNA\", \"5S ribosomal RNA\", \u76f8\u5e94\u7684 gene \u7684\u503c\u53ef\u4ee5\u662f rrsA, rrlA, rrfA ... , rr \u8868\u793a\u662f rRNA\uff0c s l f \u5206\u522b\u5bf9\u5e94 16 23 5, A\u662f\u4e00\u4e2a\u7f16\u53f7\uff0c\u4e0b\u9762\u7684\u7f16\u53f7\u662f B, C D... \u6b64\u5916\uff0c\u6bcf\u4e2a rRNA \u533a\u57df\u8981\u6709\u4e2a gene \u7684 feature\u3002 ncRNA \u7684 qualifier \u6807\u7b7e\u4e2d\u5fc5\u987b\u6709 ncRNA_class\uff0c\u7b2c 5 \u5217\u5219\u662f ncRNA \u7684\u7c7b\u522b\uff0c\u6bd4\u5982 miRNA, siRNA, scRNA \u7b49\u3002\u6b64\u5916\uff0c\u53ef\u4ee5\u4f7f\u7528 note \u4f5c\u4e3a qualifier \u7684\u6807\u7b7e\uff0c\u5176\u503c\u53ef\u968f\u610f\u6807\u793a\u3002\r\n6. mRNA \u548c CDS \u7684 product \u7684\u53d6\u503c\uff0c\u4f7f\u7528 Nr \u6ce8\u91ca\u7684\u6700\u4f18\u7ed3\u679c\u3002\u6700\u4f18\u7ed3\u679c\u5982\u679c\u5305\u542b \"hypothetical protein\" \u3001 \"predicted protein\" \u3001 \"unknown\" \u3001 \"partial\"  \u6216 \"homolog\" \u65f6\uff0c\u5219\u9700\u8981\u53d6\u5176\u5b83\u6ce8\u91ca\u7ed3\u679c\uff0c\u6216\u91c7\u53d6\u4e00\u5b9a\u7684\u63aa\u65bd\u4e86\u3002\r\n<\/pre>\n
\u539f\u6838\u751f\u7269 feature table \u7684\u8bf4\u660e\uff1ahttp:\/\/www.ncbi.nlm.nih.gov\/genbank\/genomesubmit\/#prepare_table<\/a>\u3002
\n\u539f\u6838\u751f\u7269\u7684 feature table \u7684\u8981\u70b9\uff1a<\/p>\n
\r\n1. \u5fc5\u987b\u5305\u542b\u7684 feature \u662f gene, CDS, rRNA \u548c tRNA\u3002\u4e0d\u8981\u6709 mRNA \u3002\u5e76\u4e14\uff0c\u6bcf\u4e2a CDS\uff0crRNA \u6216 tRNA \u90fd\u5c5e\u4e8e\u4e00\u4e2a gene\u3002\r\n2. Gene \u7684 qualifier \u6807\u7b7e\u5fc5\u987b\u6709 locus_tag\uff0c \u4e5f\u53ef\u4ee5\u6709 gene\u3002 gene \u7684\u503c\u4e3a gene \u7684\u540d\u79f0\uff0c\u5176\u540d\u79f0\u6709\u76f8\u5e94\u7684\u6807\u51c6\uff0c\u4ee5 3 \u4e2a\u5c0f\u5199\u5b57\u6bcd\u5f00\u59cb\u7684\u3002\r\n3. CDS \u7684 qualifier \u6807\u7b7e\u5fc5\u987b\u6709 product \u548c protein_id \u3002product \u7684\u503c\u4e5f\u6709\u76f8\u5e94\u7684\u6807\u51c6\u3002protein_id \u7684\u503c\u4e00\u822c\u4e3a gnl|xxxx|string\uff0c\u5176\u4e2d xxxx \u63a8\u8350\u662f\u5b9e\u9a8c\u5ba4\u7684\u540d\u5b57\uff0c string \u662f protein_id \u7684\u6807\u793a\uff0c\u53ef\u4ee5\u4f7f\u7528 locus_tag \u3002\r\n4. rRNA, tRNA, misc_RNA \u548c ncRNA \u90fd\u5fc5\u987b\u6709\u76f8\u5e94\u7684 gene feature\uff0c \u5176 qualifier \u5fc5\u987b\u6709 product \u3002\u4e0e RNA \u76f8\u5e94\u7684 gene \u7684 qualifier \u4e2d\uff0c\u5176 gene \u7684\u503c\uff1a5S rRNA => rrfA, 16s rRNA => rrsA, 23s rRNA => rrlA, tRNA-Lys => tRNAK, tRNA-Thr => tRNAT \u3002 rRNA \u548c tRNA \u7684\u6ce8\u91ca\u5fc5\u987b\u8981\u6709\u3002\r\n<\/pre>\n
4. <\/p>\n
4. tbl2asn \u547d\u4ee4\u751f\u6210 .sqn \u6587\u4ef6<\/h2>\n
\u5728\u5f53\u524d\u76ee\u5f55\u4e0b\u751f\u6210\u4e86 3 \u4e2a\u6587\u4ef6: species.sbt, species.fsa, specis.tbl \u3002
\n\u8fd0\u884c tbl2asn \u751f\u6210\u76ee\u6807\u6587\u4ef6 species.sqn \u3002<\/p>\n
\r\ntbl2asn -t C001.sbt -p .\/ -a s -V vb\r\n# -a s \u4e00\u4e2afasta\u6587\u4ef6\u6709\u591a\u6761\u5e8f\u5217\u65f6\uff0c\u4f7f\u7528\u6b64\u53c2\u6570\u914d\u7f6e\u3002\r\n# -V vb v\u8868\u793a\u5bf9\u8f93\u5165\u7684\u6570\u636e\u8fdb\u884c\u9a8c\u8bc1\uff0c\u751f\u6210 2 \u4e2a .val \u7684\u6587\u4ef6\uff1b-b \u751f\u6210GeneBank\u683c\u5f0f\u7684\u6587\u672c\u6587\u4ef6\uff0c\u4ee5 .gbf \u4e3a\u540e\u7f00\u3002\r\n# \u8fd0\u884c\u5b8c\u6bd5\u540e\u9700\u8981\u67e5\u770b val \u6587\u4ef6\uff0c\u5176\u4e2d\u53ef\u80fd\u6709\u5f88\u591a\u9519\u8bef\u4e0e\u8b66\u793a\u4fe1\u606f\u3002 \u6709\u4e9b\u86cb\u767d\u8d28\u5e8f\u5217\u4e0d\u662f\u4ee5 M \u5f00\u5934\uff0c\u4f1a\u5728\u6b64\u5904\u63d0\u793a ERROR \u3002\u7279\u522b\u662f\u7ec6\u83cc\u57fa\u56e0\u7ec4\u4f1a\u51fa\u73b0\u8fd9\u6837\u7684\u63d0\u793a\u3002\u5e94\u8be5\u5728 .fsa \u6587\u4ef6\u7684 header \u90e8\u5206\u52a0\u4e0a [gcode=11] \u6765\u89e3\u51b3\u3002\u8868\u660e\u5176\u9057\u4f20\u5bc6\u7801\u5b50\u8868\u662f 11 \u53f7\u3002\u6839\u636e\u9519\u8bef\uff0c\u53bb\u9664\u6240\u6709\u7684\u9519\u8bef\u63d0\u793a\u3002\r\n<\/pre>\n
\u4f7f\u7528 GenomeMacroSend \u4e0a\u4f20 .sqn \u6587\u4ef6<\/h1>\n
\u5728 GenomeMacroSend \u7f51\u9875 http:\/\/www.ncbi.nlm.nih.gov\/projects\/GenomeSubmit\/genome_submit.cgi<\/a> \u7684\u6700\u4e0b\u65b9\u7684\u8f93\u5165\u6846\u4e2d\u586b\u5199\u4fe1\u606f\u4e0a\u4f20 .sqn \u6587\u4ef6\u3002<\/p>\n
\u5168\u7f51\u9875\u65b9\u6cd5\u4e0a\u4f20\u6570\u636e<\/h1>\n
\u57fa\u56e0\u7ec4\u6570\u636e\u4e0a\u4f20\uff1aGenomes(WGS) submission portal<\/a>
\n\u8f6c\u5f55\u7ec4\u6570\u636e\u4e0a\u4f20\uff1aTSA submission portal<\/a>
\n\u4f7f\u7528\u7f51\u9875\u65b9\u5f0f\u4e0a\u4f20\u6570\u636e\u548c\u4e0a\u8ff0\u65b9\u6cd5\u57fa\u672c\u4e00\u81f4\u3002 feature tab \u7684\u5236\u4f5c\u4f9d\u7136\u9700\u8981\u81ea\u5df1\u624b\u5de5\u5236\u4f5c\uff0c\u518d\u4e0a\u4f20\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
\u521b\u5efa BioProject \u53f7\u548c BioSample \u53f7 \u5bf9\u67d0\u4e00\u4e2a\u7269\u79cd\u8fdb\u884c\u4e86\u57fa\u56e0 … \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\/2171"}],"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=2171"}],"version-history":[{"count":6,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2171\/revisions"}],"predecessor-version":[{"id":2242,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2171\/revisions\/2242"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2171"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2171"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2171"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}