{"id":18776,"date":"2013-01-24T17:22:24","date_gmt":"2013-01-24T08:22:24","guid":{"rendered":"http:\/\/www.ospn.jp\/press\/?p=18776"},"modified":"2013-03-12T16:37:08","modified_gmt":"2013-03-12T07:37:08","slug":"no32-1-useit-oss","status":"publish","type":"post","link":"https:\/\/www.ospn.jp\/press\/20130124no32-1-useit-oss.html","title":{"rendered":"\u300c\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u300d\u3092\u4f7f\u3063\u3066\u307f\u3088\u3046 (\u7b2c27\u56de \u30d5\u30ea\u30fc\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u7528\u3044\u305f\u30b2\u30ce\u30e0\u79d1\u5b66\u306b\u304a\u3051\u308b\u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u51e6\u7406)"},"content":{"rendered":"

—————————————————————————-
\n\u6771\u4eac\u8fb2\u5de5\u5927\u5b66\u30b2\u30ce\u30e0\u79d1\u5b66\u4eba\u6750\u80b2\u6210\u30d7\u30ed\u30b0\u30e9\u30e0\u7279\u4efb\u6559\u6388
\n\u77f3\u4e95 \u4e00\u592b
\n—————————————————————————-<\/p>\n

1. \u30b2\u30ce\u30e0\u79d1\u5b66\u3067\u7528\u3044\u3089\u308c\u308b\u30d5\u30ea\u30fc\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2<\/font><\/strong><\/p>\n

\u3000\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\u30fc\u3068\u3044\u3046DNA\u5869\u57fa\u914d\u5217\u60c5\u5831\u3092\u5927\u91cf\u306b\u7523\u751f\u3059\u308b\u6a5f\u5668\u304c\u5b9f\u7528\u5316
\n\u3000\u3055\u308c\u3066\u6570\u5e74\u304c\u7d4c\u904e\u3057\u3001\u30b2\u30ce\u30e0\u79d1\u5b66\u3092\u6271\u3046\u533b\u5b66\u3001\u751f\u7269\u5b66\u306e\u4e16\u754c\u3067\u306f\u65e5\u3005\u306eDNA
\n\u3000\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u306e\u7523\u751f\u91cf\u3084\u3001\u305d\u306e\u53d6\u308a\u6271\u3046\u30c7\u30fc\u30bf\u91cf\u304c\u98db\u8e8d\u7684\u306b\u5897\u3048\u3066\u3044\u307e\u3059\u3002
\n\u3000\u3053\u308c\u3089\u306e\u30c7\u30fc\u30bf\u51e6\u7406\u306b\u306fUNIX\/Linux\u3092\u4e2d\u5fc3\u3068\u3059\u308b\u30d5\u30ea\u30fc\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306f\u6b20\u304b
\n\u3000\u305b\u307e\u305b\u3093\u3002<\/p>\n

(1) \u6c4e\u7528\u306e\u30d5\u30ea\u30fc\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2<\/strong>
\n\u3000\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\u30fc\u306e\u30c7\u30fc\u30bf\u306f\u3001\u4f8b\u3048\u3070\u30a4\u30eb\u30df\u30ca\u793e\u88fd\u306e\u89e3\u6790\u6a5f\u5668\u304b\u3089\u7523\u751f
\n\u3000\u3055\u308c\u308b\u30c7\u30fc\u30bf\u306e\u5834\u5408\u30011\u30d5\u30a1\u30a4\u30eb\u3042\u305f\u308a\u306b\u6570\u5343\u4e07\u65ad\u7247\u304b\u3089\u6570\u5104\u65ad\u7247\u306eDNA
\n\u3000\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u3068\u305d\u306e\u30af\u30a6\u30a9\u30ea\u30c6\u30a3\u30c7\u30fc\u30bf\u3092\u542b\u3080\u30d5\u30a1\u30a4\u30eb\u304c\u7523\u751f\u3055\u308c\u307e\u3059\u3002
\n\u3000\u305d\u308c\u3092\u3001(1) cat\u3084grep\u3001sed\u3001awk\u306a\u3069\u306e\u30b7\u30a7\u30eb\u306e\u30b3\u30de\u30f3\u30c9\u3084\u3001(2) Perl\u3001
\n\u3000Python\u3001Ruby\u306a\u3069\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u8a00\u8a9e\u3001(3) R\u3001Octave\u306a\u3069\u306e\u7d71\u8a08\u89e3\u6790\u8a00\u8a9e
\n\u3000\u3092\u7d44\u307f\u5408\u308f\u305b\u3066\u51e6\u7406\u3057\u307e\u3059\u3002
\n\u3000\u5fc5\u8981\u306b\u5fdc\u3058\u3066\u3001(4) MySQL\u3001PostgreSQL\u306a\u3069\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3082\u4f7f\u7528\u3057\u307e\u3059\u3002
\n\u3000\u3080\u3057\u308d\u3001\u3053\u306e\u3088\u3046\u306a\u30b9\u30b1\u30fc\u30eb\u306e\u30c7\u30fc\u30bf\u89e3\u6790\u3067\u306f\u3001\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306f\u5fc5\u9808\u3067\u3059\u3002<\/p>\n

(2) \u751f\u7269\u5b66\u7684\u306a\u30c7\u30fc\u30bf\u89e3\u6790\u5c02\u7528\u306e\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2<\/strong>
\n\u3000\u3082\u3061\u308d\u3093\u3001\u751f\u7269\u5b66\u7684\u306a\u60c5\u5831\u89e3\u6790\u5c02\u7528\u306e\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3082\u591a\u6570\u958b\u767a\u3055\u308c\u3066\u3044\u307e\u3059\u3002
\n\u3000\u4f8b\u3048\u3070\u3001(1) \u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\u30fc\u304b\u3089\u7523\u751f\u3055\u308c\u305fDNA\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u3092\u4e92\u3044\u306b
\n\u3000\u30b8\u30b0\u30bd\u30fc\u30d1\u30ba\u30eb\u306e\u3088\u3046\u306b\u7d50\u5408\u3055\u305b\u3001\u9577\u3044DNA\u5869\u57fa\u914d\u5217\u3092\u5f97\u308b\u30a2\u30bb\u30f3\u30d6\u30ea\u3068\u547c\u3070
\n\u3000\u308c\u308b\u30c7\u30fc\u30bf\u89e3\u6790\u884c\u7a0b\u3067\u306f\u3001Velvet\u3001Oases\u3001Trinity\u306a\u3069\u304c\u4f7f\u7528\u3055\u308c\u307e\u3059\u3002
\n\u3000\u307e\u305f\u3001(2) \u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\u30fc\u304b\u3089\u7523\u751f\u3055\u308c\u305fDNA\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u3092\u65e2\u77e5\u306e
\n\u3000DNA\u5869\u57fa\u914d\u5217\u3078\u6574\u5217\u3055\u305b\u308b\u30de\u30c3\u30d4\u30f3\u30b0\u3068\u547c\u3070\u308c\u308b\u30c7\u30fc\u30bf\u89e3\u6790\u884c\u7a0b\u3067\u306f\u3001BWA\u3001
\n\u3000Bowtie\u306a\u3069\u304c\u4f7f\u7528\u3055\u308c\u307e\u3059\u3002<\/p>\n

\u3000(3)\u3053\u306e\u3088\u3046\u306b\u3057\u3066\u5f97\u3089\u308c\u305f\u9577\u3081\u306eDNA\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u3068\u65e2\u77e5\u306eDNA\u5869\u57fa\u914d\u5217
\n\u3000\u3068\u306e\u76f8\u540c\u6027\u306e\u691c\u7d22\u306b\u306f\u3001BLAST\u306a\u3069\u304c\u7528\u3044\u3089\u308c\u307e\u3059\u3002Perl\u3001Python\u3001Ruby\u3001
\n\u3000Java\u306a\u3069\u306b\u306f\u3001(4) \u751f\u7269\u5b66\u7684\u306a\u30c7\u30fc\u30bf\u306e\u89e3\u6790\u306b\u7279\u5316\u3057\u305f\u95a2\u6570\u306a\u3069\u3092\u96c6\u3081\u305f
\n\u3000\u30e9\u30a4\u30d6\u30e9\u30ea\u304c\u6574\u5099\u3055\u308c\u3066\u304a\u308a\u3001\u305d\u308c\u305e\u308cBioPerl\u3001BioPython\u3001BioRuby\u3001
\n\u3000BioJava\u3068\u547c\u3070\u308c\u3066\u3044\u307e\u3059\u3002
\n\u3000\u307e\u305f\u3001\u7d71\u8a08\u89e3\u6790\u30bd\u30d5\u30c8\u306eR\u306b\u306f\u3001(5) Bioconductor\u3068\u547c\u3070\u308c\u308b\u751f\u7269\u5b66\u7684\u89e3\u6790\u7528
\n\u3000\u306e\u30d1\u30c3\u30b1\u30fc\u30b8\u7fa4\u304c\u5b58\u5728\u3057\u307e\u3059\u3002<\/p>\n


\n(3) \u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u51e6\u7406\u306b\u7279\u5316\u3057\u305f\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2<\/strong>
\n\u3000\u8fd1\u5e74\u3001(1) \u30af\u30e9\u30a6\u30c9\u30b3\u30f3\u30d4\u30e5\u30fc\u30c6\u30a3\u30f3\u30b0\u3084\u4eee\u60f3\u5316\u74b0\u5883\u3092\u7d44\u307f\u5408\u308f\u305b\u305f\u30d3\u30c3\u30b0
\n\u3000\u30c7\u30fc\u30bf\u51e6\u7406\u306e\u6280\u8853\u304c\u30b2\u30ce\u30e0\u79d1\u5b66\u306b\u3082\u5fdc\u7528\u3055\u308c\u3066\u304a\u308a\u3001Hadoop\u3001OpenStack\u3001
\n\u3000Eucalyptus\u306a\u3069\u304c\u4f7f\u308f\u308c\u3066\u3044\u307e\u3059\u3002\u30b2\u30ce\u30e0\u79d1\u5b66\u306b\u304a\u3044\u3066\u306f\u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u51e6\u7406
\n\u3000\u306e\u305f\u3081\u306e\u30d5\u30a1\u30a4\u30eb\u30b7\u30b9\u30c6\u30e0\u3082\u6ce8\u76ee\u3055\u308c\u3066\u304a\u308a\u3001(2) FreeBSD\u306b\u304a\u3051\u308bZFS\u306a\u3069
\n\u3000\u30da\u30bf\u30d0\u30a4\u30c8\u7d1a\u3001\u30a8\u30af\u30b5\u30d0\u30a4\u30c8\u7d1a\u306e\u30b9\u30b1\u30fc\u30eb\u306e\u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u51e6\u7406\u3082\u8996\u91ce\u306b\u5165\u308c
\n\u3000\u305f\u6b21\u4e16\u4ee3\u30d5\u30a1\u30a4\u30eb\u30b7\u30b9\u30c6\u30e0\u306e\u5c0e\u5165\u3082\u9032\u3093\u3067\u3044\u307e\u3059\u3002\u79c1\u305f\u3061\u306e\u6559\u80b2\u30d7\u30ed\u30b0\u30e9\u30e0
\n\u3000\u3067\u30b2\u30ce\u30e0\u30c7\u30fc\u30bf\u89e3\u6790\u306b\u4f7f\u7528\u3057\u3066\u3044\u308b\u4e3b\u306a\u30d5\u30ea\u30fc\u30bd\u30d5\u30c8\u3092\u8868\uff11\u306b\u793a\u3057\u307e\u3059\u3002<\/p>\n

\u8868\uff1a\u6771\u4eac\u8fb2\u5de5\u5927\u5b66\u30b2\u30ce\u30e0\u79d1\u5b66\u4eba\u6750\u80b2\u6210\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u30c7\u30fc\u30bf\u89e3\u6790\u306b\u7528\u3044\u308b\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u7fa4
\nTable\uff1aSoftware for Genomic Data Analysis used in Tokyo University of Agriculture and Technology<\/p>\n\n\n\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\u3000\u7528\u9014<\/td>\n\u3000\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2<\/td>\n<\/tr>\n
\u3000OS<\/td>\n\u3000Linux\/UNIX
\n\u3000(CentOS 6.3,
\n\u3000 Scientific Linux 6.3 and FreeBSD 9)<\/td>\n<\/tr>\n
\u3000\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u8a00\u8a9e<\/td>\n\u3000Perl, Python, Ruby,
\n\u3000Java, C, C++<\/td>\n<\/tr>\n
\u3000\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9<\/td>\n\u3000MySQL, PostgreSQL<\/td>\n<\/tr>\n
\u3000\u30b2\u30ce\u30e0\u914d\u5217\u30c7\u30fc\u30bf\u306e\u30a2\u30bb\u30f3\u30d6\u30ea<\/td>\n\u3000Velvet, ABySS, SOAPdenovo,
\n\u3000WGS Assembler, MIRA3, Phrap<\/td>\n<\/tr>\n
\u3000\u30b2\u30ce\u30e0\u914d\u5217\u30c7\u30fc\u30bf\u306e\u30de\u30c3\u30d4\u30f3\u30b0<\/td>\n\u3000Bowtie, Bowtie2, BWA, SOAP<\/td>\n<\/tr>\n
\u3000RNA \u767a\u73fe\u89e3\u6790\u7528\u30bd\u30d5\u30c8<\/td>\n\u3000Tophat, Cufflinks, Trinity,
\n\u3000Oases, SOAPdenovo-Trans<\/td>\n
\u3000ChIP-Seq\u89e3\u6790\u7528\u30bd\u30d5\u30c8<\/td>\n\u3000MACS, Quest, SISSRs, SPP<\/td>\n<\/tr>\n
\u3000\u7d71\u8a08\u89e3\u6790\u30bd\u30d5\u30c8<\/td>\n\u3000R\/Bioconductor, Octave<\/td>\n<\/tr>\n
\u3000\u76f8\u540c\u6027\u89e3\u6790\u3001\u6ce8\u91c8\u4ed8\u3051\u30bd\u30d5\u30c8<\/td>\n\u3000BLAST, BLAT<\/td>\n<\/tr>\n
\u3000\u7dcf\u5408DNA\u89e3\u6790\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2<\/td>\n\u3000EMBOSS<\/td>\n<\/tr>\n
\u3000\u751f\u7269\u5b66\u30c7\u30fc\u30bf\u89e3\u6790\u7528\u30e9\u30a4\u30d6\u30e9\u30ea<\/td>\n\u3000BioPerl, BioRuby, BioPython, BioJava<\/td>\n<\/tr>\n
\u3000\u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u89e3\u6790\u7528\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2<\/td>\n\u3000Hadoop, OpenStack, Eucalyptus<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

\n2. \u30b2\u30ce\u30e0\u79d1\u5b66\u306b\u304a\u3051\u308b\u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u89e3\u6790<\/font><\/strong><\/p>\n

\u3000\u73fe\u5728\u306f\u3001\u30b2\u30ce\u30e0\u79d1\u5b66\u3067\u6271\u3046DNA\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u306e\u30d5\u30a1\u30a4\u30eb\u306e\u30b5\u30a4\u30ba\u306f\u6570\u767e\u30e1\u30ac
\n\u3000\u30d0\u30a4\u30c8\u304b\u3089\u6570\u5341\u30ae\u30ac\u30d0\u30a4\u30c8\u306e\u30b5\u30a4\u30ba\u306e\u3082\u306e\u304c\u591a\u304f\u3001\u3053\u308c\u306f\u30d5\u30a1\u30a4\u30eb\u306e\u884c\u6570\u3067\u8868\u73fe
\n\u3000\u3059\u308b\u3068\u6570\u4e07\u884c\u304b\u3089\u6570\u5104\u884c\u304f\u3089\u3044\u3067\u3059\u3002
\n\u3000\u3053\u308c\u3089\u3092Perl\u3001Python\u3001Ruby\u306a\u3069\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u8a00\u8a9e\u3084R\u3001Octave\u306a\u3069\u306e\u7d71\u8a08\u89e3\u6790
\n\u3000\u30bd\u30d5\u30c8\u3001BLAST\u306a\u3069\u306eDNA\u5869\u57fa\u914d\u5217\u89e3\u6790\u306e\u5c02\u7528\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3067\u30c7\u30fc\u30bf\u51e6\u7406\u3092\u3059\u308b
\n\u3000\u5834\u5408\u306b\u3001\u30e1\u30e2\u30ea\u4e0d\u8db3\u3068\u306a\u308a\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u5b9f\u884c\u52d5\u4f5c\u304c\u6975\u7aef\u306b\u9045\u304f\u306a\u3063\u305f\u308a\u3001\u30cf\u30f3
\n\u3000\u30b0\u30a2\u30c3\u30d7\u3092\u8d77\u3053\u3057\u305f\u308a\u3068\u3044\u3046\u3053\u3068\u304c\u983b\u7e41\u306b\u767a\u751f\u3057\u307e\u3059\u3002<\/p>\n

\u3000\u30e1\u30e2\u30ea\u3092\u5897\u3084\u3059\u306a\u3069\u306e\u30cf\u30fc\u30c9\u9762\u306e\u5145\u5b9f\u306b\u3088\u308a\u3053\u308c\u3089\u306e\u89e3\u6790\u3092\u53ef\u80fd\u306b\u3059\u308b\u3053\u3068\u3082
\n\u3000\u3067\u304d\u307e\u3059\u304c\u3001\u30d5\u30a1\u30a4\u30eb\u3092\u5206\u5272\u3057\u3066\u5358\u4f4d\u30d7\u30ed\u30bb\u30b9\u5f53\u305f\u308a\u306e\u30c7\u30fc\u30bf\u91cf\u3092\u5c0f\u3055\u304f\u3057\u3001
\n\u3000\u4e26\u5217\u51e6\u7406\u3084\u30d0\u30c3\u30c1\u51e6\u7406\u306b\u3088\u308b\u76f4\u5217\u51e6\u7406\u3092\u7d44\u307f\u5408\u308f\u305b\u308b\u3053\u3068\u306b\u3088\u308a\u3001\u52b9\u7387\u7684\u306b\u89e3
\n\u3000\u6790\u3092\u884c\u3048\u307e\u3059\u3002\u8fd1\u5e74\u306f\u3001\u30b3\u30a2\u6570\u304c\u591a\u3044CPU\u3092\u642d\u8f09\u3057\u305f\u30b3\u30f3\u30d4\u30e5\u30fc\u30bf\u304c\u5897\u3048\u3066\u3044
\n\u3000\u308b\u306e\u3067\u3001\u305d\u308c\u3092\u6d3b\u7528\u3057\u305f\u89e3\u6790\u6226\u7565\u304c\u6709\u52b9\u3060\u3068\u601d\u308f\u308c\u307e\u3059\u3002<\/p>\n

\n3. \u30b2\u30ce\u30e0\u79d1\u5b66\u306b\u304a\u3051\u308b\u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u89e3\u6790\u306e\u4f8b<\/font><\/strong><\/p>\n

\u3000\u30b2\u30ce\u30e0\u30c7\u30fc\u30bf\u3067\u3088\u304f\u884c\u308f\u308c\u308b\u4f5c\u696d\u306f\u3001\u30d5\u30a1\u30a4\u30eb\u5f62\u5f0f\u306e\u5909\u63db\u3067\u3059\u3002
\n\u3000\u3053\u3053\u3067\u306f\u3001\u52d5\u4f5c\u306f\u305d\u308c\u307b\u3069\u901f\u304f\u306a\u3044\u306e\u3067\u3001\u3042\u307e\u308a\u5b9f\u7528\u7684\u3067\u306f\u3042\u308a\u307e\u305b\u3093\u304c\u3001
\n\u3000\u3072\u3068\u3064\u306e\u7df4\u7fd2\u4f8b\u3068\u3057\u3066R\u3068Perl\u3092\u30b7\u30a7\u30eb\u30b9\u30af\u30ea\u30d7\u30c8\u3068\u7d44\u307f\u5408\u308f\u305b\u3066GFF\u3068\u3044\u3046
\n\u3000\u30d5\u30a1\u30a4\u30eb\u5f62\u5f0f\u304b\u3089\u3001\u907a\u4f1d\u5b50\u306e\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u3092\u53ce\u7d0d\u3057\u305f\u30de\u30eb\u30c1fasta\u3068\u3044\u3046\u5f62\u5f0f\u306e
\n\u3000\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210\u3059\u308b\u65b9\u6cd5\u4f8b\u3092\u3054\u7d39\u4ecb\u3057\u307e\u3059\u3002
\n\u3000\u3053\u3053\u3067\u3054\u7d39\u4ecb\u3059\u308b\u65b9\u6cd5\u306f\u6700\u5584\u306e\u4f8b\u3067\u306f\u3042\u308a\u307e\u305b\u3093\u3057\u3001Perl\u306e\u4ee3\u308f\u308a\u306bRuby\u3084Python\u3092
\n\u3000\u4f7f\u3046\u3053\u3068\u3082\u53ef\u80fd\u3067\u3057\u3087\u3046\u3002<\/p>\n

\u3000\u307e\u305f\u3001\u3072\u3068\u3064\u306e\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u8a00\u8a9e\u3067\u3059\u3079\u3066\u306e\u30d7\u30ed\u30bb\u30b9\u5b8c\u7d50\u3055\u305b\u308b\u3053\u3068\u3082\u53ef\u80fd
\n\u3000\u3067\u3059\u3057\u3001\u540c\u69d8\u306e\u64cd\u4f5c\u3092\u884c\u3063\u3066\u304f\u308c\u308b\u30c4\u30fc\u30eb\u30ad\u30c3\u30c8\uff08\u65e2\u5b58\u306e\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u30d1\u30c3\u30b1\u30fc\u30b8\uff09
\n\u3000\u3082\u5b58\u5728\u3059\u308b\u3068\u601d\u3044\u307e\u3059\u3002
\n\u3000\u3057\u304b\u3057\u3001\u305d\u3053\u307e\u3067\u3084\u3089\u306a\u304f\u3066\u3082\u3001\u65e5\u5e38\u306e\u4f55\u6c17\u306a\u3044\u4f5c\u696d\u306e\u306a\u304b\u3067\u3001\u7279\u306b\u7279\u6b8a\u306a\u30a2\u30d7\u30ea
\n\u3000\u30b1\u30fc\u30b7\u30e7\u30f3\u3092\u4f7f\u7528\u3057\u306a\u304f\u3066\u3082\u77ed\u6642\u9593\u3067\u3055\u3089\u308a\u3068\u51e6\u7406\u3067\u304d\u3066\u4fbf\u5229\u3067\u3059\u3002<\/p>\n

\n(1)\u3000\u30b2\u30ce\u30e0DNA\u306e\u5869\u57fa\u914d\u5217\u60c5\u5831\u3068\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u306e\u5165\u624b<\/strong>
\n\u3000\u3053\u3053\u3067\u306f\u3001\u30e2\u30c7\u30eb\u751f\u7269\u3067\u3042\u308b\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u30b2\u30ce\u30e0DNA\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u3068
\n\u3000\uff08\u907a\u4f1d\u5b50\u306e\u4f4d\u7f6e\u60c5\u5831\u3092\u793a\u3059\uff09\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u30c7\u30fc\u30bf\u304b\u3089\u3001\u5404\u907a\u4f1d\u5b50\u306e\u30de\u30eb\u30c1
\n\u3000fasta\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210\u3057\u307e\u3059\u3002
\n\u3000\u4f5c\u6210\u306b\u5fc5\u8981\u306a\u30c7\u30fc\u30bf\u3092\u542b\u3080\u30d5\u30a1\u30a4\u30eb\u3092\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u3057\u3066\u5165\u624b\u3057\u307e\u3059\u3002<\/p>\n

\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u30b2\u30ce\u30e0DNA\u5869\u57fa\u914d\u5217\u30c7\u30fc\u30bf\u306e\u5165\u624b<\/p>\n

$ wget ftp:\/\/ftp.arabidopsis.org\/home\/tair\/Sequences\/whole_chromosomes\/TAIR10* <\/pre>\n
\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\uff08\u907a\u4f1d\u5b50\u306e\u4f4d\u7f6e\u60c5\u5831\u3092\u793a\u3059\uff09\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u30c7\u30fc\u30bf\u306e\u5165\u624b<\/p>\n
$ wget ftp:\/\/ftp.arabidopsis.org\/home\/tair\/Genes\/TAIR10_genome_release\/TAIR10_gff3\/TAIR10_GFF3_genes.gff<\/pre>\n
\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u5f97\u3089\u308c\u305f\u30d5\u30a1\u30a4\u30eb\u304c\u78ba\u8a8d\u3067\u304d\u307e\u3059\u3002<\/p>\n
$ ls\r\nTAIR10_GFF3_genes.gff  TAIR10_chr2.fas  TAIR10_chr4.fas  TAIR10_chrC.fas\r\nTAIR10_chr1.fas        TAIR10_chr3.fas  TAIR10_chr5.fas  TAIR10_chrM.fas<\/pre>\n
\n(2)\u3000\u30b2\u30ce\u30e0DNA\u5869\u57fa\u914d\u5217\u60c5\u5831\u3092\u30c7\u30fc\u30bf\u62bd\u51fa\u3057\u3084\u3059\u3044\u3088\u3046\u306b\u52a0\u5de5<\/strong>
\n\u307e\u305a\u3001\u67d3\u8272\u4f53\u3054\u3068\u306efasta\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u30b3\u30de\u30f3\u30c9cat\u3067\u3072\u3068\u3064\u306e\u30d5\u30a1\u30a4\u30eb
\n\u201dTAIR10.fas\u201d\u306b\u307e\u3068\u3081\u307e\u3059\u3002<\/p>\n
$ cat *fas | sed -e '\/^$\/d' >> TAIR10.fas\r\n$ ls\r\nTAIR10.fas             TAIR10_chr2.fas  TAIR10_chr5.fas\r\nTAIR10_GFF3_genes.gff  TAIR10_chr3.fas  TAIR10_chrC.fas\r\nTAIR10_chr1.fas        TAIR10_chr4.fas  TAIR10_chrM.fas<\/pre>\n
TAIR10.fas\u3092\u3001\uff1c\u914d\u5217\u540d\uff1e\u30bf\u30d6\uff1c\u914d\u5217\uff1e\u306e\u3088\u3046\u306a\u5f62\u306b\u6210\u5f62\u3059\u308b\u305f\u3081\u306b\u3001
\n\u4ee5\u4e0b\u306e\u3088\u3046\u306aPerl\u30b9\u30af\u30ea\u30d7\u30c8\u201dgetIDseq.pl\u201d\u3092\u6e96\u5099\u3057\u3066\u304a\u304d\u307e\u3059\u3002<\/p>\n
$ vi getIDseq.pl<\/p>\n
#!\/usr\/bin\/perl\r\n# name: getIDSeq.pl\r\n# usage:\r\n# perl getIDSeq.pl input_filename > output_filename\r\n\r\n$input = $ARGV[0];\r\n\r\nopen ( FILEHANDLE ,  "< $input");\r\n\r\n@array = <FILEHANDLE> ;\r\nchomp(@array);\r\n\r\nfor (my $i = 0; $i <= $#array; $i++){\r\n    if ($array[$i] =~ \/^>\/) {\r\n        if ($i == 0) {\r\n            print "$array[$i]\\t";\r\n        } else {\r\n            print "\\n$array[$i]\\t";\r\n        }\r\n    } else {\r\n        print "$array[$i]";\r\n    }\r\n}\r\n\r\nprint "\\n";\r\n\r\nclose(FILEHANDLE);<\/pre>\n
\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3059\u308b\u3053\u3068\u306b\u3088\u308a\u3001\uff1c\u914d\u5217\u540d\uff1e\u30bf\u30d6\uff1c\u914d\u5217\uff1e\u306e
\n\u3088\u3046\u306a\u5f62\u306e\u30d5\u30a1\u30a4\u30eb\u201cID_seq.txt\u201d\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n
$ perl getIDseq.pl TAIR10.fas | awk -F"\\t" '{print substr($1,2,4)"\\t"$2}' | sed -e 's\/chlo\/ChrC\/g' | sed -e's\/mito\/ChrM\/g' > ID_seq.txt<\/pre>\n
\u201cID_seq.txt\u201d\u306f\u3001\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u306b\u306a\u308a\u307e\u3059\u3002
\n\u67d3\u8272\u4f53\u540d\u3068\u5869\u57fa\u914d\u5217\u306e\u9593\u306f\u30bf\u30d6\u3067\u533a\u5207\u3089\u308c\u3066\u3044\u307e\u3059\u3002<\/p>\n
Chr1\t<\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u7b2c1\u756a\u67d3\u8272\u4f53\u30b2\u30ce\u30e0\u306e\u5869\u57fa\u914d\u5217>
\nChr2\t<\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u7b2c\uff12\u756a\u67d3\u8272\u4f53\u30b2\u30ce\u30e0\u306e\u5869\u57fa\u914d\u5217>
\nChr3\t<\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u7b2c\uff13\u756a\u67d3\u8272\u4f53\u30b2\u30ce\u30e0\u306e\u5869\u57fa\u914d\u5217>
\nChr4\t<\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u7b2c\uff14\u756a\u67d3\u8272\u4f53\u30b2\u30ce\u30e0\u306e\u5869\u57fa\u914d\u5217>
\nChr5\t<\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u7b2c\uff15\u756a\u67d3\u8272\u4f53\u30b2\u30ce\u30e0\u306e\u5869\u57fa\u914d\u5217>
\nChrC\t<\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u8449\u7dd1\u4f53\u30b2\u30ce\u30e0\u306e\u5869\u57fa\u914d\u5217>
\nChrM\t<\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u30df\u30c8\u30b3\u30f3\u30c9\u30ea\u30a2\u30b2\u30ce\u30e0\u306e\u5869\u57fa\u914d\u5217><\/p>\n
\n(3)\u3000\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u60c5\u5831\u304b\u3089\u3001\u8ee2\u5199\u7523\u7269\u306e\u4f4d\u7f6e\u60c5\u5831\u3092\u62bd\u51fa<\/strong>
\n\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u30d5\u30a1\u30a4\u30eb\u201dTAIR10_GFF3_genes.gff\u201d\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u3063\u3066
\n\u3044\u307e\u3059\u3002\u5b9f\u306e\u3068\u3053\u308d\u3001\u3053\u308c\u304b\u3089\u30b3\u30de\u30f3\u30c9grep\u304bawk\u3092\u4f7f\u3063\u3066\u201cgene\u201d\u3068\u3044\u3046
\n\u5358\u8a9e\u3092\u542b\u3080\u884c\u3092\u96c6\u3081\u308c\u3070\u7c21\u5358\u306b\u907a\u4f1d\u5b50\u306e\u958b\u59cb\u4f4d\u7f6e\u3068\u7d42\u4e86\u4f4d\u7f6e\u306e\u4f4d\u7f6e\u60c5\u5831\u3092
\n\u53d6\u308a\u51fa\u305b\u307e\u3059\u3002\u3057\u304b\u3057\u3001\u4eca\u56de\u306f\u7df4\u7fd2\u306e\u610f\u5473\u3082\u3042\u308a\u3001exon\u306e\u60c5\u5831\u3057\u304b\u306a\u304b\u3063\u305f
\n\u3068\u4eee\u5b9a\u3057\u3066\u3001\u305d\u306e\u60c5\u5831\u304b\u3089\u5404\u907a\u4f1d\u5b50\u306e\u958b\u59cb\u4f4d\u7f6e\u3068\u7d42\u4e86\u4f4d\u7f6e\u306e\u60c5\u5831\u3092\u53d6\u308a\u51fa\u3059
\n\u65b9\u6cd5\u3092\u3054\u7d39\u4ecb\u3057\u307e\u3059\u3002<\/p>\n
$ head TAIR10_GFF3_genes.gff\r\nChr1\tTAIR10\tchromosome\t1\t30427671\t.\t.\t.\tID=Chr1;Name=Chr1\r\nChr1\tTAIR10\tgene\t3631\t5899\t.\t+\t.\tID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010\r\nChr1\tTAIR10\tmRNA\t3631\t5899\t.\t+\t.\tID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1\r\nChr1\tTAIR10\tprotein\t3760\t5630\t.\t+\t.\tID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1\r\nChr1\tTAIR10\texon\t3631\t3913\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\tfive_prime_UTR\t3631\t3759\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\tCDS\t3760\t3913\t.\t+\t0\tParent=AT1G01010.1,AT1G01010.1-Protein;\r\nChr1\tTAIR10\texon\t3996\t4276\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\tCDS\t3996\t4276\t.\t+\t2\tParent=AT1G01010.1,AT1G01010.1-Protein;\r\nChr1\tTAIR10\texon\t4486\t4605\t.\t+\t.\tParent=AT1G01010.1<\/pre>\n
\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u30d5\u30a1\u30a4\u30eb\u201dTAIR10_GFF3_genes.gff\u201d\u306e\u3046\u3061exon\u306e\u60c5\u5831\u3060\u3051\u3092
\n\u53d6\u308a\u51fa\u3059\u5834\u5408\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3057\u307e\u3059\u3002<\/p>\n
$ cat TAIR10_GFF3_genes.gff | awk '($3=="exon"){print}' | head\r\nChr1\tTAIR10\texon\t3631\t3913\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\texon\t3996\t4276\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\texon\t4486\t4605\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\texon\t4706\t5095\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\texon\t5174\t5326\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\texon\t5439\t5899\t.\t+\t.\tParent=AT1G01010.1\r\nChr1\tTAIR10\texon\t8571\t8737\t.\t-\t.\tParent=AT1G01020.1\r\nChr1\tTAIR10\texon\t8417\t8464\t.\t-\t.\tParent=AT1G01020.1\r\nChr1\tTAIR10\texon\t8236\t8325\t.\t-\t.\tParent=AT1G01020.1\r\nChr1\tTAIR10\texon\t7942\t7987\t.\t-\t.\tParent=AT1G01020.1<\/pre>\n
\u4e0a\u8a18\u306e\u30c7\u30fc\u30bf\u306e\u3046\u3061\u4eca\u56de\u306e\u89e3\u6790\u306b\u5fc5\u8981\u306a\u60c5\u5831\u306f\u3001\u907a\u4f1d\u5b50\u540d\u3068\u67d3\u8272\u4f53\u540d\u3001\u5404exon\u306e
\n\u958b\u59cb\u4f4d\u7f6e\u3068\u7d42\u4e86\u4f4d\u7f6e\u3067\u3059\u3002
\n\u305d\u306e\u60c5\u5831\u3092\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3092\u7528\u3044\u3066\u62bd\u51fa\u3057\u3001\u201dexon_list.txt\u201d\u3068\u3057\u3066\u4fdd\u5b58\u3057\u307e\u3059\u3002<\/p>\n
$ cat TAIR10_GFF3_genes.gff | awk '($3=="exon"){print $9"\\t"$1"\\t"$4"\\t"$5}' | sed -e 's\/Parent=\/\/g' | head\r\nAT1G01010.1\tChr1\t3631\t3913\r\nAT1G01010.1\tChr1\t3996\t4276\r\nAT1G01010.1\tChr1\t4486\t4605\r\nAT1G01010.1\tChr1\t4706\t5095\r\nAT1G01010.1\tChr1\t5174\t5326\r\nAT1G01010.1\tChr1\t5439\t5899\r\nAT1G01020.1\tChr1\t8571\t8737\r\nAT1G01020.1\tChr1\t8417\t8464\r\nAT1G01020.1\tChr1\t8236\t8325\r\nAT1G01020.1\tChr1\t7942\t7987\r\n$ cat TAIR10_GFF3_genes.gff | awk '($3=="exon"){print $9"\\t"$1"\\t"$4"\\t"$5}' | sed -e 's\/Parent=\/\/g' > exon_list.txt<\/pre>\n
\u201dexon_list.txt\u201d\u304b\u3089\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3092\u7528\u3044\u3066\u3001
\n\u907a\u4f1d\u5b50\u540d\u3060\u3051\u3092\u62bd\u51fa\u3057\u3001\u201dgene_name.list\u201d\u3068\u3044\u3046\u540d\u524d\u3067\u4fdd\u5b58\u3057\u307e\u3059\u3002<\/p>\n
$ cat exon_list.txt | cut -f1 | sort | uniq | head\r\nAT1G01010.1\r\nAT1G01020.1\r\nAT1G01020.2\r\nAT1G01030.1\r\nAT1G01040.1\r\nAT1G01040.2\r\nAT1G01046.1\r\nAT1G01050.1\r\nAT1G01060.1\r\nAT1G01060.2\r\n$ cat exon_list.txt | cut -f1 | sort | uniq > gene_name.list<\/pre>\n
\u907a\u4f1d\u5b50\u306f\u3001\u4ee5\u4e0b\u306e\u3088\u3046\u306b40745\u7a2e\u985e\u5b58\u5728\u3059\u308b\u3053\u3068\u304c\u308f\u304b\u308a\u307e\u3059\u3002<\/p>\n
$ cat  gene_name.list | wc -l\r\n40745<\/pre>\n
\u6b21\u306b\u3001Genes\u3068\u3044\u3046\u30d5\u30a9\u30eb\u30c0\u3092\u4f5c\u308a\u3001<\/p>\n
$ mkdir Genes<\/pre>\n
\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30b3\u30de\u30f3\u30c9\u3092\u3001<\/p>\n
$ cat exon_list.txt | grep AT1G01010.1 > Genes\/AT1G01010.1.txt<\/pre>\n
awk\u3092\u7528\u3044\u3066\u907a\u4f1d\u5b50\u540d\u306b\u5bfe\u5fdc\u3059\u308b\u3088\u3046\u306b\u4f5c\u6210\u3057\u3001
\n\u201cmakeGenes.sh\u201d\u3068\u3044\u3046\u540d\u524d\u3067\u4fdd\u5b58\u3057\u307e\u3059\u3002<\/p>\n
$ head Gene_name.list | awk '{print "cat exon_list.txt | grep "$1" > Gene\/"$1".txt"}'\r\ncat exon_list.txt | grep AT1G01010.1 > Genes\/AT1G01010.1.txt\r\ncat exon_list.txt | grep AT1G01020.1 > Genes\/AT1G01020.1.txt\r\ncat exon_list.txt | grep AT1G01020.2 > Genes\/AT1G01020.2.txt\r\ncat exon_list.txt | grep AT1G01030.1 > Genes\/AT1G01030.1.txt\r\ncat exon_list.txt | grep AT1G01040.1 > Genes\/AT1G01040.1.txt\r\ncat exon_list.txt | grep AT1G01040.2 > Genes\/AT1G01040.2.txt\r\ncat exon_list.txt | grep AT1G01046.1 > Genes\/AT1G01046.1.txt\r\ncat exon_list.txt | grep AT1G01050.1 > Genes\/AT1G01050.1.txt\r\ncat exon_list.txt | grep AT1G01060.1 > Genes\/AT1G01060.1.txt\r\ncat exon_list.txt | grep AT1G01060.2 > Genes\/AT1G01060.2.txt\r\n$ cat transcript_name.list | awk '{print "cat exon_list.txt | grep "$1" > Genes\/"$1".txt"}' > makeTrans.sh<\/pre>\n
\u4ee5\u4e0b\u306e\u3088\u3046\u306b40745\u884c\u306e\u30b7\u30a7\u30eb\u30b9\u30af\u30ea\u30d7\u30c8\u304c\u3067\u304d\u308b\u306e\u3067\u3001<\/p>\n
$ wc -l makeGenes.sh\r\n40745 makeGenes.sh<\/pre>\n
\u305d\u308c\u3092\u5b9f\u884c\u3057\u307e\u3059\u3002<\/p>\n
$ sh makeGenes.sh<\/pre>\n
\u3059\u308b\u3068\u3001\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u907a\u4f1d\u5b50\u3054\u3068\u306b\u5206\u304b\u308c\u305f40745\u500b\u306e\u30d5\u30a1\u30a4\u30eb\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n
$ ls Genes | head\r\nAT1G01010.1.txt\r\nAT1G01020.1.txt\r\nAT1G01020.2.txt\r\nAT1G01030.1.txt\r\nAT1G01040.1.txt\r\nAT1G01040.2.txt\r\nAT1G01046.1.txt\r\nAT1G01050.1.txt\r\nAT1G01060.1.txt\r\nAT1G01060.2.txt\r\n$ ls Genes | wc -l\r\n40745\r\n$ cat Genes\/AT1G01010.1.txt\r\nAT1G01010.1\tChr1\t3631\t3913\r\nAT1G01010.1\tChr1\t3996\t4276\r\nAT1G01010.1\tChr1\t4486\t4605\r\nAT1G01010.1\tChr1\t4706\t5095\r\nAT1G01010.1\tChr1\t5174\t5326\r\nAT1G01010.1\tChr1\t5439\t5899<\/pre>\n
\u4e0a\u8a18\u306e3\u5217\u76ee\u30684\u5217\u76ee\u306e\u6570\u5024\u7fa4\u306e\u6700\u5c0f\u5024\u3068\u6700\u5927\u5024\u304c\u3001\u907a\u4f1d\u5b50AT1G01010.1\u306e
\n\u958b\u59cb\u4f4d\u7f6e\u3001\u7d42\u4e86\u4f4d\u7f6e\u3068\u3044\u3046\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002\u3053\u308c\u3092\u7d71\u8a08\u89e3\u6790\u30bd\u30d5\u30c8R\u3067
\n\u5bfe\u8a71\u7684\u306b\u884c\u3046\u3068\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u3057\u3066\u6c42\u3081\u3089\u308c\u307e\u3059\u3002<\/p>\n
$ cd Genes\/\r\n$ R\r\n> in_f <- "AT1G01010.1.txt"\r\n> out_f <- "AT1G01010.1.out.txt"\r\n> data <- read.table(in_f, sep="\\t", quote="")\r\n> pos <- c(data[,3], data[,4])\r\n> write.table(cbind(data[1,1:2],min(pos),max(pos)), out_f, sep="\\t", append=F, quote=F, row.names=F)\r\n> q()\r\nSave workspace image? [y\/n\/c]: y\r\n$ cat AT1G01010.1.out.txt\r\nV1\tV2\tmin(pos)\tmax(pos)\r\nAT1G01010.1\tChr1\t3631\t5899<\/pre>\n
\u3053\u308c\u3092\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u540d\u3068\u51fa\u529b\u30d5\u30a1\u30a4\u30eb\u540d\u3092\u6307\u5b9a\u3057\u3066\u3001
\nR\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3067\u66f8\u304f\u3068\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n
$ vi GeneExt.R\r\nargs <- commandArgs(trailingOnly = T)\r\nin_f <- args[1] \r\nout_f <- args[2]\r\ndata <- read.table(in_f, sep="\\t", quote="") \r\npos <- c(data[,3], data[,4])\r\nwrite.table(cbind(data[1,1:2],min(pos),max(pos)), out_f, sep="\\t", append=F, quote=F, row.names=F) \r\nq()<\/pre>\n
GeneExt.R\u3092\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3092\u7528\u3044\u3066\u5b9f\u884c\u3057\u307e\u3059\u3002<\/p>\n
$ R --vanilla --slave --args AT1G01020.1.txt AT1G01020.1.out.txt < GeneExt.R<\/pre>\n
\u3059\u308b\u3068\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u7d50\u679c\u304c\u5f97\u3089\u308c\u307e\u3059\u3002<\/p>\n
$ cat AT1G01020.1.txt\r\nAT1G01020.1\tChr1\t8571\t8737\r\nAT1G01020.1\tChr1\t8417\t8464\r\nAT1G01020.1\tChr1\t8236\t8325\r\nAT1G01020.1\tChr1\t7942\t7987\r\nAT1G01020.1\tChr1\t7762\t7835\r\nAT1G01020.1\tChr1\t7564\t7649\r\nAT1G01020.1\tChr1\t7384\t7450\r\nAT1G01020.1\tChr1\t7157\t7232\r\nAT1G01020.1\tChr1\t6437\t7069\r\nAT1G01020.1\tChr1\t5928\t6263\r\n$ cat AT1G01020.1.out.txt\r\nV1\tV2\tmin(pos)\tmax(pos)\r\nAT1G01020.1\tChr1\t5928\t8737<\/pre>\n
\u3053\u3053\u3067\u3001awk\u3092\u4f7f\u3063\u3066\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u66f8\u304d\u3001
\n\u201cGeneExt.sh\u201d\u3068\u3044\u3046\u540d\u524d\u3067\u4fdd\u5b58\u3057\u307e\u3059\u3002<\/p>\n
$ cat gene_name.list | awk '{print "R --vanilla --slave --args "$1".txt "$1".out.txt < GeneExt.R"}' | head\r\nR --vanilla --slave --args AT1G01010.1.txt AT1G01010.1.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01020.1.txt AT1G01020.1.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01020.2.txt AT1G01020.2.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01030.1.txt AT1G01030.1.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01040.1.txt AT1G01040.1.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01040.2.txt AT1G01040.2.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01046.1.txt AT1G01046.1.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01050.1.txt AT1G01050.1.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01060.1.txt AT1G01060.1.out.txt < GeneExt.R\r\nR --vanilla --slave --args AT1G01060.2.txt AT1G01060.2.out.txt < GeneExt.R\r\n$ cat gene_name.list | awk '{print "R --vanilla --slave --args "$1".txt "$1".out.txt < GeneExt.R"}' > GeneExt.sh<\/pre>\n
GeneExt.sh\u3092\u3001\u30d5\u30a1\u30a4\u30ebGenes\u5185\u306b\u79fb\u52d5\u3055\u305b\u3001\u5b9f\u884c\u3057\u307e\u3059\u3002<\/p>\n
$ mv GeneExt.sh Genes\/\r\n$ cd Genes\/\r\n$ sh GeneExt.sh<\/pre>\n
\u7d42\u4e86\u5f8c\u3001\u30b3\u30de\u30f3\u30c9cat\u3092\u7528\u3044\u3066\u201c.out.txt\u201d\u3092\u542b\u3080\u30d5\u30a1\u30a4\u30eb\u3092\u3059\u3079\u3066
\n\u30de\u30fc\u30b8\u3057\u3001\u30b3\u30de\u30f3\u30c9grep\u3092\u7528\u3044\u3066\u201dAT\u201d\u3067\u59cb\u307e\u3063\u3066\u3044\u308b\u884c\u3060\u3051\u3092\u96c6\u3081\u3066\u3001
\nGenes.txt\u3092\u5f97\u307e\u3059\u3002<\/p>\n
$ cat *.out.txt | grep \u201c^AT\u201d > Genes.txt<\/pre>\n
\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u3001\u5404\u907a\u4f1d\u5b50\u306e\u67d3\u8272\u4f53\u4e0a\u306e\u4f4d\u7f6e\u60c5\u5831\u306e\u30ea\u30b9\u30c8\u304c\u5f97\u3089\u308c\u307e\u3057\u305f\u3002<\/p>\n
$ head Genes.txt \r\nAT1G01010.1\tChr1\t3631\t5899\r\nAT1G01020.1\tChr1\t5928\t8737\r\nAT1G01020.2\tChr1\t6790\t8737\r\nAT1G01030.1\tChr1\t11649\t13714\r\nAT1G01040.1\tChr1\t23146\t31227\r\nAT1G01040.2\tChr1\t23416\t31120\r\nAT1G01046.1\tChr1\t28500\t28706\r\nAT1G01050.1\tChr1\t31170\t33153\r\nAT1G01060.1\tChr1\t33666\t37840\r\nAT1G01060.2\tChr1\t33666\t37780<\/pre>\n
\n(4) \u30b2\u30ce\u30e0\u306eDNA\u5869\u57fa\u914d\u5217\u304b\u3089\u907a\u4f1d\u5b50\u306eDNA\u5869\u57fa\u914d\u5217\u3092\u5207\u308a\u51fa\u3057\u3001
\n\u3000 \u30de\u30eb\u30c1fasta\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u308b<\/strong>
\n\u6700\u5f8c\u306b\u3001 Genes.txt\u306e\u907a\u4f1d\u5b50\u306e\u4f4d\u7f6e\u60c5\u5831\u3092\u3082\u3068\u306bID_seq.txt\u304b\u3089\u3001\u5404\u907a\u4f1d\u5b50\u914d\u5217\u30c7\u30fc\u30bf\u3092\u5207\u308a\u51fa\u3057\u3001\u30de\u30eb\u30c1 fasta\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u308b\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u4f5c\u6210\u3057\u3001\u5b9f\u884c\u3057\u307e\u3059\u3002\u3053\u308c\u304b\u3089\u5f8c\u306e\u64cd\u4f5c\u306f\u3001\u539f\u7a3f\u306e\u679a\u6570\u304c\u591a\u304f\u306a\u3063\u3066\u304d\u305f\u306e\u3067\u3001\u3053\u308c\u306f\u8aad\u8005\u3078\u306e\u5bbf\u984c\u3068\u3057\u3066\u304a\u304d\u307e \u3057\u3087\u3046\u3002<\/p>\n
\u30d2\u30f3\u30c8\u3068\u3057\u3066\u306f\u3001Perl\u3084Ruby\u306b\u3088\u308b\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u7528\u3044\u3066\u4f5c\u6210\u3059\u308b\u3053\u3068\u3082\u53ef\u80fd\u3067\u3059\u3057\uff08Perl\u3067\u3059\u3068substr\u95a2\u6570\u3092\u7528\u3044\u3066\u3067\u304d\u307e\u3059\u3057\u3001Ruby\u3067\u3059\u3068str[2..4]\u306e\u3088\u3046\u306b\u6dfb\u5b57\u3092\u7528\u3044\u3066\u7c21\u5358\u306b\u3067\u304d\u307e\u3059\u3002\uff09\u3001cut\u306a\u3069\u306e\u30b7\u30a7\u30eb\u306e\u30b3\u30de\u30f3\u30c9\u3092\u30aa\u30d7\u30b7\u30e7\u30f3\u201c-c\u201d\u7528\u3044\u3066\u4f5c\u6210\u3059\u308b\u3053\u3068\u3082\u53ef\u80fd\u3067\u3059\u3002\u3053\u308c\u3089\u4e00\u9023\u306e\u64cd\u4f5c\u306f\u3001\u5f53\u7136\u306e\u3053\u3068\u306a\u304c\u3089\u3001\u30b7\u30a7\u30eb\u30b9\u30af\u30ea\u30d7\u30c8\u3084Perl\u306a\u3069\u306e\u5358\u4e00\u30b9\u30af\u30ea\u30d7\u30c8\u8a00\u8a9e\u3092\u7528\u3044\u3066\u3059\u3079\u3066\u8a18\u8ff0\u3057\u672c\u683c\u7684\u306a\u30d7\u30ed\u30b0\u30e9\u30e0\u3068\u3059\u308b\u3053\u3068\u3082\u53ef\u80fd\u3067\u3059\u3002\u5b9f\u969b\u306b\u3001\u3044\u308d\u3044\u308d\u306a\u8a00\u8a9e\u3067\u540c\u69d8\u306e\u52d5\u4f5c\u3092\u3059\u308b\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u4f5c\u6210\u3057\u3001\u901f\u5ea6\u3092\u6bd4\u8f03\u3057\u305f\u308a\u3057\u3066\u6700\u9069\u5316\u3059\u308b\u3053\u3068\u3082\u3042\u308a\u307e\u3059\u3002
\n\u3057\u304b\u3057\u3001\u3053\u3053\u3067\u7d39\u4ecb\u3057\u305f\u7c21\u4fbf\u306a\u65b9\u6cd5\u3067\u3044\u308d\u3044\u308d\u306a\u8a00\u8a9e\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u30b7\u30a7\u30eb\u30b9\u30af\u30ea\u30d7\u30c8\u3067\u7d44\u307f\u5408\u308f\u305b\u308b\u3053\u3068\u306b\u3088\u308a\u3001\u601d\u3044\u3064\u3044\u305f\u64cd\u4f5c\u3092\u3059\u3050\u306b\u30b9\u30af\u30ea\u30d7\u30c8\u3067\u66f8\u3051\u307e\u3059\u3002\u3057\u305f\u304c\u3063\u3066\u3001\u8a08\u7b97\u91cf\u304c\u5c11\u306a\u304f\u3059\u3050\u306b\u7b54\u3048\u3092\u51fa\u3057\u305f\u3044\u5834\u5408\u306b\u306f\u3001\u91cd\u5b9d\u3057\u307e\u3059\u3002<\/p>\n
\n\u307e\u3068\u3081<\/font><\/strong>
\n\u4ee5\u4e0a\u306e\u3088\u3046\u306b\u3001\u3044\u308d\u3044\u308d\u306a\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u8a00\u8a9e\u3084\u89e3\u6790\u30c4\u30fc\u30eb\u3092\u30b7\u30fc\u30e0\u30ec\u30b9\u306b\u7d44\u307f\u5408\u308f\u305b\u3066\u3001\u60c5\u5831\u3092\u62bd\u51fa\u3059\u308b\u3053\u3068\u304c\u53ef\u80fd\u3067\u3059\u3002\u3053\u308c\u3089\u306e\u7a4d\u307f\u91cd\u306d\u306f\u3001\u672c\u683c\u7684\u306a\u30d3\u30c3\u30b0\u30c7\u30fc\u30bf\u89e3\u6790\u306b\u3082\u3064\u306a\u304c\u3063\u3066\u3044\u304d\u3001\u52b9\u7387\u7684\u306a\u89e3\u6790\u30b7\u30b9\u30c6\u30e0\u306e\u78ba\u7acb\u306b\u3082\u751f\u304b\u3055\u308c\u308b\u3082\u306e\u3068\u8003\u3048\u3066\u3044\u307e\u3059\u3002<\/p>\n
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OSC2013 Tokyo\/Spring\u306b\u51fa\u5c55\u3057\u307e\u3059\u3002
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\n\u25bc\u5c55\u793a\u4e00\u89a7
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