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Bioinformatics Training(BGI, BJ) - 华大基因生物信息培训材料(In Chinese)

Bioinformatics Training(BGI, BJ) - 华大基因生物信息培训材料(In Chinese)

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Published by Chiucheng Liu
Bioinformatics Training Materials for Beijing Genomics Institute (Huada)- 华大基因生物信息培训材料

This training material is distributed as an inner institute manual, it's not for commercial purposes. Copyrights reserved by Beijing Genomics Institute (Beijing Huada). Contact BGI-Shenzhen for further information.

本培训资料版权归华大基因(北京)所有,此版本仅用于学术交流,不得用于商业用途。如有疑问,请联系深圳华大基因研究院。


深圳华大基因研究院
地址:深圳市盐田区北山工业区综合楼
电话:0755-25273620
传真:0755-25273620

BGI-Shenzhen
Address: Comprehensive building, Beishan Industry Garden, Yantian District, Shenzhen, P.R. China
Tel: 755-25273620
Fax: 755-25273620
Bioinformatics Training Materials for Beijing Genomics Institute (Huada)- 华大基因生物信息培训材料

This training material is distributed as an inner institute manual, it's not for commercial purposes. Copyrights reserved by Beijing Genomics Institute (Beijing Huada). Contact BGI-Shenzhen for further information.

本培训资料版权归华大基因(北京)所有,此版本仅用于学术交流,不得用于商业用途。如有疑问,请联系深圳华大基因研究院。


深圳华大基因研究院
地址:深圳市盐田区北山工业区综合楼
电话:0755-25273620
传真:0755-25273620

BGI-Shenzhen
Address: Comprehensive building, Beishan Industry Garden, Yantian District, Shenzhen, P.R. China
Tel: 755-25273620
Fax: 755-25273620

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Published by: Chiucheng Liu on Nov 22, 2008
Copyright:Attribution Non-commercial

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05/09/2014

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\u751f\u7269\u4fe1\u606f\u5b66\u57f9\u8bad\u6559\u6750
\u5317\u4eac\u534e\u5927\u57fa\u56e0\u7814\u7a76\u4e2d\u5fc3
\u76ee\u5f55

\u7b2c1 \u7ae0Unix/Linux\u64cd\u4f5c\u7cfb\u7edf\u4ecb\u7ecd............................................................................................................4 1.1 \u6587\u4ef6\u548c\u76ee\u5f55\u76f8\u5173.........................................................................................................................4 1.2 \u538b\u7f29\u548c\u89e3\u538b\u7f29.............................................................................................................................4 1.3 \u8fdb\u7a0b\u53ca\u5176\u4ed6................................................................................................................................5 1.4 \u8fdc\u7a0b\u767b\u9646....................................................................................................................................6

1.5\u8f6f\u4ef6\u5b89\u88c5\u7b80\u4ecb............................................................................................................................12
\u7b2c 2 \u7ae0 \u6570\u636e\u7684\u57fa\u672c\u5904\u7406.........................................................................................................................13
2.1 \u6d4b\u5e8f\u539f\u7406\u4ecb\u7ecd............................................................................................................................13

2.2 \u5cf0\u56fe\u8f6c\u5316 Phred........................................................................................................................13
2.3 Phd2Fasta................................................................................................................................20
2.4 \u8f7d\u4f53\u5c4f\u853d Crossmatch..............................................................................................................23
2.5 \u5e8f\u5217\u805a\u7c7b\u62fc\u63a5...........................................................................................................................29
2.5.1 Phrap.............................................................................................................................29
2.5.2 Cap3..............................................................................................................................39
2.6 Consed......................................................................................................................................43
2.7 Primer3....................................................................................................................................57

\u7b2c 3 \u7ae0 \u5e8f\u5217\u7684\u6bd4\u5bf9................................................................................................................................62
3.1 \u5168\u5c40\u6bd4\u5bf9..................................................................................................................................62

3.1.1 Clustalw...........................................................................................................................62 3.1.2 MUSCLE.........................................................................................................................78 3.1.3 HMMER..........................................................................................................................81

3.2 \u5c40\u90e8\u6bd4\u5bf9..................................................................................................................................85

3.2.1 Blast.................................................................................................................................85 3.2.2 blat...................................................................................................................................98 3.2.3 blastz..............................................................................................................................104 3.2.4 GeneWise....................................................................................................................... 110 3.2.5 Fasta............................................................................................................................... 119 3.2.6 Exonerate.......................................................................................................................127 3.2.7 Sim4............................................................................................................................... 132

\u7b2c 4 \u7ae0 \u57fa\u56e0\u7ec4/\u57fa\u56e0\u7684\u6ce8\u91ca.................................................................................................................140

4.1 \u91cd\u590d\u5e8f\u5217\u5206\u6790.........................................................................................................................140
4.1.1 RepeatMasker.............................................................................................................140
4.1.2 Trf..............................................................................................................................151
4.1.3 LTR_STRUC...................................................................................................................155
4.2 RNA\u5206\u6790..................................................................................................................................158
4.2.1 tRNAScan.....................................................................................................................158
4.2.2 MicroRNA.....................................................................................................................163
4.2.3 snoRNA.........................................................................................................................171
4.2.4 rRNA\uff08rfam\uff09.............................................................................................................175
4.3 \u57fa\u56e0\u9884\u6d4b................................................................................................................................179
4.3.1 Glimmer.......................................................................................................................179
4.3.2 GlimmerM.....................................................................................................................184
4.3.3 Genscan.......................................................................................................................188
4.3.4 TwinScan.....................................................................................................................191
4.3.5 BGF..............................................................................................................................193
4.3.6 Fgenesh.......................................................................................................................196
4.4 \u57fa\u56e0\u529f\u80fd\u6ce8\u91ca.........................................................................................................................198
4.4.1 InterproScan.............................................................................................................198
4.4.2 WEGO............................................................................................................................203

\u7b2c 5 \u7ae0 SNP\u5206\u6790....................................................................................................................................209

5.1 Polyphred..................................................................................................................................209 5.2 SNPdetector..............................................................................................................................215 5.3 CrossMatch...............................................................................................................................221

\u7b2c 6 \u7ae0 \u8fdb\u5316\u5206\u6790\u4e13\u9898...........................................................................................................................224

6.1 Phylip........................................................................................................................................224 6.2 Paml..........................................................................................................................................230 6.3 KaKs_Calculator.......................................................................................................................237 6.4 FGF........................................................................................................................................... 244 6.5 mega..........................................................................................................................................257

\u7b2c 7 \u7ae0 \u57fa\u56e0\u8868\u8fbe\u5206\u6790\u4e13\u9898...................................................................................................................261

7.1 EST(Expressed Sequence Tag)\u8868\u8fbe\u5e8f\u5217\u6807\u7b7e\uff08EST\uff09\u5206\u6790.............................................261
7.1.1 EST\u57fa\u672c\u4ecb\u7ecd...............................................................................................................261
7.1.2 EST\u5206\u6790\u6d41\u7a0b\u4ecb\u7ecd.......................................................................................................264
7.1.3 EST\u7684\u5e94\u7528...................................................................................................................278
7.1.4 \u5b9e\u4f8b............................................................................................................................279
7.1.5 \u53c2\u8003\u6587\u732e.....................................................................................................................280
7.2 \u751f\u7269\u82af\u7247(Microarray)\u5206\u6790.................................................................................................280
7.2.1 \u80cc\u666f\u4ecb\u7ecd.....................................................................................................................280
7.2.2 \u82af\u7247\u7684\u6570\u636e\u5206\u6790.........................................................................................................283
7.2.3 \u82af\u7247Oligo\u8bbe\u8ba1...........................................................................................................298
7.3 Motif\u9884\u6d4b..............................................................................................................................300
7.3.1 MEME/MAST\u7cfb\u7edf...........................................................................................................300
7.3.2 MDScan.........................................................................................................................315
\u7b2c8 \u7ae0 \u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b.......................................................................................................................318

8.1\u86cb\u767d\u8d28 \u7ed3\u6784\u77e5\u8bc6\u4ecb\u7ecd...........................................................................................................318 8.2\u86cb\u767d\u8d28 \u7ed3\u6784\u9884\u6d4b\u65b9\u6cd5...........................................................................................................327 8.3\u86cb\u767d\u8d28 \u7ed3\u6784\u9884\u6d4b\u7684Threading\u65b9\u6cd5..................................................................................328 8.4\u86cb\u767d\u8d28 \u4e09\u7ef4\u7ed3\u6784\u9884\u6d4b\u6d41\u7a0b\u4ecb\u7ecd...........................................................................................328

\u7b2c 9 \u7ae0 \u516c\u7528\u6570\u636e\u5e93\u4ecb\u7ecd.......................................................................................................................341

9.1 NCBI.........................................................................................................................................341 9.2 UCSC........................................................................................................................................351 9.3 Ensembl....................................................................................................................................357

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