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详细说明： 第 1 章 Unix/Linux操作系统介绍...........................................................................................................1 1.1 远程登陆...................................................................................................................................1 1.2 文件的复制、删除和移动命令................................................................................................7 1.3 目录的创建、删除及更改目录命令........................................................................................9 1.4 文本查看命令............................ .............................................................................................11 1.5 文本处理命令.........................................................................................................................13 1.6 改变文件或目录的权限命令..................................................................................................16 1.7 备份与压缩命令.....................................................................................................................18 1.8 磁盘及系统管理.....................................................................................................................20 1.9 软件安装简介.........................................................................................................................22 1.10 其他......................................................................................................................................23 第2 章 数据的基本处理........................................................................................................................25 2.1 测序原理介绍..........................................................................................................................25 2.2 峰图转化 Phred ......................................................................................................................27 2.3 Phd2Fasta ...............................................................................................................................32 2.4 载体屏蔽 cross_match ..........................................................................................................36 2.5 序列聚类拼接.........................................................................................................................43 2.5.1 Phrap ..........................................................................................................................43 2.5.2 Cap3 ............................................................................................................................50 2.6 Consed ....................................................................................................................................54 2.7 Primer3 ..................................................................................................................................68 第3 章 序列的比对...............................................................................................................................73 3.1 全局比对................................................................................................................................76 3.1.1 Clustalw ....................................................................................................................76 3.1.2 MUSCLE ........................................................................................................................93 3.1.3 HMMER ..........................................................................................................................99 3.2 局部比对...............................................................................................................................103 3.2.1 Blast ........................................................................................................................103 3.2.2 blat ..........................................................................................................................117 3.2.3 blastz ......................................................................................................................123 3.2.4 GeneWise ..................................................................................................................130 3.2.5 Fasta ........................................................................................................................138 3.2.6 Exonerate ................................................................................................................147 3.2.7 Sim4 ..........................................................................................................................152 第4 章 基因组/基因的注释................................................................................................................160 4.1 重复序列分析.......................................................................................................................160 4.1.1 RepeatMasker ..........................................................................................................161 4.1.2 Trf ............................................................................................................................172 4.1.3 LTR_STRUC ................................................................................................................177 4.2 RNA分析................................................................................................................................179 4.2.1 tRNAScan ..................................................................................................................180 4.2.2 MicroRNA ..................................................................................................................185 4.2.3 snoRNA ......................................................................................................................193 4.2.4 rRNA（rfam） ..........................................................................................................198 4.3 基因预测...............................................................................................................................202 4.3.1 Glimmer ....................................................................................................................205 4.3.2 GlimmerM ..................................................................................................................210 4.3.3 Genscan ....................................................................................................................215 4.3.4 TwinScan ..................................................................................................................218 4.3.5 BGF ............................................................................................................................221 4.3.6 Fgenesh ....................................................................................................................223 4.4 基因功能注释.......................................................................................................................225 4.4.1 InterproScan ..........................................................................................................225 4.4.2 WEGO ..........................................................................................................................231 第5 章 SNP分析...................................................................................................................................236 5.1 Polyphred .............................................................................................................................237 5.2 SNPdetector .........................................................................................................................243 5.3 cross_match .........................................................................................................................250 第6 章 进化分析专题..........................................................................................................................253 6.1 Phylip ..................................................................................................................................255 6.2 Paml ......................................................................................................................................261 6.3 KaKs_Calculator .................................................................................................................267 6.4 FGF ........................................................................................................................................275 6.5 mega ......................................................................................................................................289 第7 章 基因表达分析专题..................................................................................................................293 7.1 EST(Expressed Sequence Tag)表达序列标签分析..........................................................293 7.1.1 EST基本介绍............................................................................................................293 7.1.2 EST分析流程介绍....................................................................................................296 7.1.3 BGI EST Pipeline(BEP)介绍................................................................................309 7.1.4 EST的应用................................................................................................................316 7.2 生物芯片(Microarray)分析................................................................................................318 7.2.1 背景介绍..................................................................................................................318 7.2.2 芯片的数据分析......................................................................................................320 7.2.3 芯片Oligo设计........................................................................................................333 7.3 Motif预测.............................................................................................................................335 7.3.1 MEME/MAST系统........................................................................................................335 7.3.2 MDScan ......................................................................................................................351 Motif预测小结....................................................................................................................353 第8 章 蛋白质结构预测......................................................................................................................355 8.1 蛋白质结构知识介绍...........................................................................................................355 8.2 蛋白质结构预测方法...........................................................................................................362 8.3 蛋白质结构预测的Threading方法......................................................................................363 8.4 蛋白质三维结构预测流程介绍............................................................................................363 ...展开收缩
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