{"id":27538,"date":"2024-02-01T16:59:30","date_gmt":"2024-02-01T08:59:30","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27538"},"modified":"2024-02-01T16:59:32","modified_gmt":"2024-02-01T08:59:32","slug":"%e8%a7%a3%e5%86%b3%e9%87%8d%e5%a4%8d%e5%ba%8f%e5%88%97%e6%b3%a8%e9%87%8a%e9%9a%be%e9%a2%98%ef%bc%8c%e7%94%a8repeatmodeler%e5%92%8crepeatmasker%e5%b0%b1%e5%a4%9f%e4%ba%86%ef%bc%81%ef%bc%88%e4%ba%8c","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27538","title":{"rendered":"\u89e3\u51b3\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\u96be\u9898\uff0c\u7528RepeatModeler\u548cRepeatMasker\u5c31\u591f\u4e86\uff01\uff08\u4e8c\uff09"},"content":{"rendered":"<p>hello\uff0c\u4e0a\u4e00\u7bc7\u6211\u4eec\u8bb2\u4e86\u5982\u4f55\u5b89\u88c5\u548c\u914d\u7f6eRepeatModeler\u4ee5\u53caRepeatMasker\u8fd9\u4e24\u4e2a\u8f6f\u4ef6\uff0c\u600e\u4e48\u6837\uff0c\u4f60\u6709\u6ca1\u6709\u548c\u5c0f\u679c\u4e00\u8d77\u5b89\u88c5\u5b8c\u6210\u5462\uff1f\u4eca\u5929\u6211\u4eec\u8fdb\u5165\u6211\u4eec\u7684\u6b63\u9898\uff0c\u4e5f\u5c31\u662f\u5982\u4f55\u7ec4\u5408\u4f7f\u7528\u8fd9\u4e24\u4e2a\u8f6f\u4ef6\u5bf9\u76ee\u6807\u57fa\u56e0\u7ec4\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\uff0c\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\uff01<\/p>\n<p><strong>\u4ec0\u4e48\u662f\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\uff1f<\/strong><\/p>\n<p>\u5728\u5bf9\u76ee\u6807\u57fa\u56e0\u7ec4\u57fa\u56e0\u7ec4\u8fdb\u884c\u6ce8\u91ca\u524d\uff0c\u5c0f\u679c\u6765\u4ecb\u7ecd\u4e00\u4e0b\u4ec0\u4e48\u662f\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\uff1a<\/p>\n<p>\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\u662f\u6307\u5bf9\u57fa\u56e0\u7ec4\u4e2d\u7684\u91cd\u590d\u5e8f\u5217\u8fdb\u884c\u8bc6\u522b\u3001\u5206\u7c7b\u548c\u6807\u8bb0\u7684\u8fc7\u7a0b\u3002\u5728\u57fa\u56e0\u7ec4\u4e2d\uff0c\u91cd\u590d\u5e8f\u5217\u662f\u6307\u5728DNA\u5e8f\u5217\u4e2d\u5b58\u5728\u591a\u6b21\u91cd\u590d\u51fa\u73b0\u7684\u7247\u6bb5\uff0c\u53ef\u4ee5\u5305\u62ec\u7b80\u5355\u91cd\u590d\u5e8f\u5217\uff08\u5982\u77ed\u4e32\u8054\u91cd\u590d\u3001\u5fae\u536b\u661f\u7b49\uff09\u548c\u590d\u6742\u91cd\u590d\u5e8f\u5217\uff08\u5982\u8f6c\u5ea7\u5b50\u3001LTR\u53cd\u8f6c\u5f55\u8f6c\u5ea7\u5b50\u7b49\uff09\u3002\u91cd\u590d\u5e8f\u5217\u5728\u57fa\u56e0\u7ec4\u7684\u7ed3\u6784\u548c\u529f\u80fd\u4e2d\u8d77\u7740\u91cd\u8981\u7684\u4f5c\u7528\u3002<\/p>\n<p>\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\u8fc7\u7a0b\u901a\u5e38\u4f7f\u7528\u5404\u79cd\u8ba1\u7b97\u65b9\u6cd5\u548c\u5de5\u5177\u6765\u5b8c\u6210\uff0c\u5176\u4e2d\u5305\u62ec\u91cd\u590d\u5e8f\u5217\u6570\u636e\u5e93\u7684\u6bd4\u5bf9\u3001\u6a21\u5f0f\u5339\u914d\u3001\u5e8f\u5217\u6bd4\u8f83\u3001\u673a\u5668\u5b66\u4e60\u7b49\u6280\u672f\u3002\u6ce8\u91ca\u7684\u76ee\u6807\u662f\u786e\u5b9a\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e2d\u54ea\u4e9b\u90e8\u5206\u662f\u91cd\u590d\u5e8f\u5217\uff0c\u5e76\u63d0\u4f9b\u5173\u4e8e\u8fd9\u4e9b\u91cd\u590d\u5e8f\u5217\u7684\u76f8\u5173\u4fe1\u606f\u3002<\/p>\n<p>\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\u53ef\u4ee5\u63d0\u4f9b\u4ee5\u4e0b\u4fe1\u606f\uff1a<\/p>\n<ul>\n<li><strong>\u91cd\u590d\u5e8f\u5217\u7684\u4f4d\u7f6e\uff1a<\/strong>\u6ce8\u91ca\u4f1a\u6307\u793a\u91cd\u590d\u5e8f\u5217\u5728\u57fa\u56e0\u7ec4\u4e2d\u7684\u5177\u4f53\u4f4d\u7f6e\uff0c\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u4e86\u89e3\u5b83\u4eec\u5728\u57fa\u56e0\u7ec4\u4e2d\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/li>\n<li><strong>\u91cd\u590d\u5e8f\u5217\u7684\u7c7b\u522b\uff1a<\/strong>\u6ce8\u91ca\u53ef\u4ee5\u5c06\u91cd\u590d\u5e8f\u5217\u5206\u4e3a\u4e0d\u540c\u7684\u7c7b\u522b\uff0c\u5982\u4f4e\u590d\u6742\u5ea6\u5e8f\u5217\u3001\u8f6c\u5ea7\u5b50\u7b49\uff0c\u4ee5\u4fbf\u66f4\u597d\u5730\u7406\u89e3\u5b83\u4eec\u7684\u6027\u8d28\u548c\u529f\u80fd\u3002<\/li>\n<li><strong>\u91cd\u590d\u5e8f\u5217\u7684\u6570\u91cf\u548c\u957f\u5ea6\uff1a<\/strong>\u6ce8\u91ca\u53ef\u4ee5\u63d0\u4f9b\u91cd\u590d\u5e8f\u5217\u7684\u6570\u91cf\u548c\u957f\u5ea6\u7edf\u8ba1\u4fe1\u606f\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u4e86\u89e3\u5b83\u4eec\u5728\u57fa\u56e0\u7ec4\u4e2d\u7684\u4e30\u5ea6\u548c\u5927\u5c0f\u3002<\/li>\n<li><strong>\u91cd\u590d\u5e8f\u5217\u7684\u5bb6\u65cf\u5173\u7cfb\uff1a<\/strong>\u6ce8\u91ca\u53ef\u4ee5\u5c06\u76f8\u4f3c\u7684\u91cd\u590d\u5e8f\u5217\u805a\u7c7b\u6210\u5bb6\u65cf\uff0c\u5e76\u63d0\u4f9b\u5b83\u4eec\u4e4b\u95f4\u7684\u5bb6\u65cf\u5173\u7cfb\u4fe1\u606f\uff0c\u6709\u52a9\u4e8e\u7814\u7a76\u91cd\u590d\u5e8f\u5217\u7684\u8fdb\u5316\u548c\u8d77\u6e90\u3002<\/li>\n<\/ul>\n<p>\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u5173\u4e8e\u57fa\u56e0\u7ec4\u7ed3\u6784\u3001\u6f14\u5316\u548c\u529f\u80fd\u7684\u91cd\u8981\u4fe1\u606f\uff0c\u5bf9\u4e8e\u8fdb\u4e00\u6b65\u7406\u89e3\u57fa\u56e0\u7ec4\u7684\u7ec4\u6210\u548c\u673a\u5236\u5177\u6709\u91cd\u8981\u610f\u4e49\u3002<\/p>\n<p><strong>RepeatModeler+RepeatMasker\u7ec4\u5408\u4f7f\u7528<\/strong><\/p>\n<p><strong>\u6570\u636e\u51c6\u5907<\/strong><\/p>\n<p>\u5bf9\u4e8e\u6211\u4eec\u5373\u5c06\u6ce8\u91ca\u7684\u6570\u636e\u6587\u4ef6\uff0c\u5927\u5bb6\u53ef\u4ee5\u901a\u8fc7NCBI\u5b98\u7f51\u641c\u7d22\u81ea\u5df1\u611f\u5174\u8da3\u7684\u7269\u79cd\u5bf9\u5e94\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u5e76\u4e0b\u8f7d\u5373\u53ef\u54e6\uff0c\u5728\u8fd9\u91cc\u5c0f\u679c\u4ee5\u9999\u8549\u6700\u65b0\u53d1\u5e03\u7684\u5b8c\u6574\u57fa\u56e0\u7ec4\u6587\u4ef6\uff08DH pahang\u683d\u57f9\u54c1\u79cd\uff09\u4e3a\u4f8b\uff0c\u5728\u8fd9\u91cc\u7ed9\u51fa\u4e0b\u8f7d\u94fe\u63a5\uff1a<\/p>\n<p><a href=\"https:\/\/banana-genome-hub.southgreen.fr\/bio_data\/1\">Musa acuminata malaccensis | Banana Genome Hub (southgreen.fr)<\/a><\/p>\n<p><strong>RepeatModeler\u6784\u5efa\u91cd\u590d\u5e8f\u5217\u5e93<\/strong><\/p>\n<p>\u5728\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca\u524d\uff0c\u6211\u4eec\u9700\u8981\u4f7f\u7528RepeatModeler\u6765\u9884\u6d4b\u57fa\u56e0\u7ec4\u91cd\u590d\u5e8f\u5217\uff0c\u4ee5\u4e3a\u4e0b\u4e00\u6b65\u7684RepeatMasker\u5efa\u7acb\u91cd\u590d\u5e8f\u5217\u5e93\uff0c\u5177\u4f53\u7684\u64cd\u4f5c\u4e3b\u8981\u5206\u4e3a\u4ee5\u4e0b\u4e09\u6b65\uff1a<\/p>\n<p><strong>\u5efa\u5e93<\/strong><\/p>\n<p>step1\uff1a<\/p>\n<p>.\/BuildDatabase -name musa1 -engine ncbi \/share\/home\/xiongchu\/downloads\/complete-gene-multi\/banana\/Musa_acuminata_pahang_v4.fasta<br \/>\n# -engine ncbi\uff1a \u8868\u793a\u4f7f\u7528rmblast\u4e3a\u641c\u7d22\u5f15\u64ce<br \/>\n# -name musa1\uff1a \u8868\u793a\u5efa\u7acb\u6570\u636e\u5e93\u7684\u540d\u5b57\u4e3amusa1<br \/>\n# Musa_acuminata_pahang_v4.fasta\uff1a\u9999\u8549\u57fa\u56e0\u7ec4\u6587\u4ef6<\/p>\n<p>\u64cd\u4f5c\u5b8c\u6210\u540e\uff0c\u6211\u4eec\u5f97\u5230\u4ee5\u4e0b\u6587\u4ef6\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"153\" class=\"wp-image-27539\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-5.png?resize=640%2C153\" alt=\"\u6587\u672c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-5.png?w=1152 1152w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-5.png?resize=300%2C72 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-5.png?resize=1024%2C245 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-5.png?resize=768%2C184 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-5.png?resize=600%2C144 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u5176\u5b83\u53c2\u6570\u8bf4\u660e\uff1a<\/p>\n<p>#\u5efa\u5e93\uff0c\u5229\u7528rice \u4e00\u4e2a\u5b9e\u4f8bfasta\u6587\u4ef6<br \/>\nBuildDatablase \u2013name ricedb \u2013engine ncbi rice.sample.2.fa<br \/>\n\u200b<br \/>\n#\u53c2\u6570\u8bf4\u660e<br \/>\n-name &lt;database name&gt;<br \/>\nThe name of the database to create.<br \/>\n-engine &lt;engine name&gt;<br \/>\nThe name of the search engine we are using. I.e abblast\/wublast or rmblast.<br \/>\n-dir &lt;directory&gt;<br \/>\nThe name of a directory containing fasta files to be processed. The<br \/>\nfiles are recognized by their suffix. Only *.fa and *.fasta files<br \/>\nare processed.<br \/>\n-batch &lt;file&gt;<br \/>\nThe name of a file which contains the names of fasta files to<br \/>\nprocess. The files names are listed one per line and should be fully<br \/>\nqualified.<br \/>\n\u200b<br \/>\nRepeatModeler -database ricedb -pa 5<br \/>\n\u200b<br \/>\n#\u53c2\u6570\u8bf4\u660e<br \/>\n-database<br \/>\nThe name of the sequence database to run an analysis on. This is the<br \/>\nname that was provided to the BuildDatabase script using the &#8220;-name&#8221;<br \/>\noption.<br \/>\n-pa #<br \/>\nSpecify the number of parallel search jobs to run. RMBlast jobs will<br \/>\nuse 4 cores each and ABBlast jobs will use a single core each. i.e.<br \/>\non a machine with 12 cores and running with RMBlast you would use<br \/>\n-pa 3 to fully utilize the machine.<br \/>\n-recoverDir &lt;Previous Output Directory&gt;<br \/>\nIf a run fails in the middle of processing, it may be possible<br \/>\nrecover some results and continue where the previous run left off.<br \/>\nSimply supply the output directory where the results of the failed<br \/>\nrun were saved and the program will attempt to recover and continue<br \/>\nthe run.<\/p>\n<p>step2\uff1a<\/p>\n<p>.\/RepeatModeler -database musa1 -engine ncbi -pa 20 &amp;&gt; musa1.out &amp;<br \/>\n# -database \u8981\u548c\u4e0a\u4e00\u6b65\u4e00\u81f4<br \/>\n# -engine \u8981\u548c\u4e0a\u4e00\u6b65\u4e00\u81f4<br \/>\n# -pa \u8868\u793a\u7ebf\u7a0b\u6570<\/p>\n<p>\u8fd9\u4e00\u6b65\u7684\u64cd\u4f5c\u9700\u8981\u7684\u65f6\u95f4\u8f83\u957f\uff0c\u5927\u5bb6\u8010\u5fc3\u7b49\u5f85\u54e6~<\/p>\n<p>\u64cd\u4f5c\u5b8c\u6210\u540e\u5c06\u4ea7\u751f\u4ee5\u4e0b\u6587\u4ef6\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"101\" class=\"wp-image-27540\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?resize=640%2C101\" alt=\"\u6587\u672c\n\n\u4f4e\u53ef\u4fe1\u5ea6\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?w=1545 1545w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?resize=300%2C47 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?resize=1024%2C162 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?resize=768%2C121 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?resize=1536%2C243 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?resize=600%2C95 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-6.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u800c\u5bf9\u4e8e\u4e4b\u540e\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\u5de5\u4f5c\uff0c\u6211\u4eec\u8981\u7528\u5230\u7684\u6587\u4ef6\u4e5f\u5c31\u662fmusa1-families.fa\u6587\u4ef6\uff0c\u4f5c\u4e3a\u6211\u4eec\u4ea7\u751f\u7684\u91cd\u590d\u5e8f\u5217\u5e93\u6587\u4ef6\u3002<\/p>\n<p><strong>RepeatMasker\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u6ce8\u91ca<\/strong><\/p>\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528RepeatMasker\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u7684\u6ce8\u91ca\u5de5\u4f5c\u4e86\uff0c\u5728\u6267\u884c\u6ce8\u91ca\u547d\u4ee4\u4e4b\u524d\uff0c\u9700\u8981\u63d0\u524d\u521b\u5efa\u4e00\u4e2a\u6587\u4ef6\u5939\u6765\u5b58\u653e\u6211\u4eec\u6ce8\u91ca\u540e\u7684\u7ed3\u679c\u6587\u4ef6\u54e6\uff0c\u5728\u8fd9\u91cc\u5c0f\u679c\u521b\u5efa\u4e86\u540d\u4e3abnrpt\u7684\u6587\u4ef6\u5939\u4f5c\u4e3a\u7ed3\u679c\u6587\u4ef6\u5939\uff0c\u5927\u5bb6\u6839\u636e\u81ea\u5df1\u7684\u60c5\u51b5\u6765\u521b\u5efa\u54e6\uff01<\/p>\n<p>\u7136\u540e\u6211\u4eec\u6267\u884c\u4ee5\u4e0b\u547d\u4ee4<\/p>\n<p>.\/RepeatMasker -e rmblast -lib \/share\/home\/xiongchu\/downloads\/repeat-soft\/RepeatModeler-2.0.1\/musa1-families.fa -pa 16 -dir bnrpt1 \/share\/home\/xiongchu\/downloads\/complete-gene-multi\/banana\/Musa_acuminata_pahang_v4.fasta<br \/>\n\u200b<br \/>\n\u603b\u7ed3\uff1a<br \/>\n\u64cd\u4f5c\u547d\u4ee4\u7684\u57fa\u672c\u8bed\u6cd5\u4e3a\uff1a<br \/>\n.\/RepeatMasker -e \u641c\u7d22\u5f15\u64ce\u540d\u79f0 -lib \u91cd\u590d\u5e8f\u5217\u5e93\u7684\u8def\u5f84 -pa \u5e76\u884c\u7ebf\u7a0b\u6570 -dir \u7ed3\u679c\u6587\u4ef6\u5939\u540d\u79f0 \u57fa\u56e0\u7ec4\u6587\u4ef6\u8def\u5f84<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"101\" class=\"wp-image-27541\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-7.png?resize=640%2C101\" alt=\"\u6587\u672c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" 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