目录
第 1 章 Unix/Linux操作系统介绍............................................................................................................4
1.1 文件和目录相关.........................................................................................................................4
1.2 压缩和解压缩.............................................................................................................................4
1.3 进程及其他 ................................................................................................................................5
1.4 远程登陆 ....................................................................................................................................6
1.5 软件安装简介............................................................................................................................12
第 2 章 数据的基本处理.........................................................................................................................13
2.1 测序原理介绍............................................................................................................................13
2.2 峰图转化 Phred........................................................................................................................13
2.3 Phd2Fasta ................................................................................................................................20
2.4 载体屏蔽 Crossmatch..............................................................................................................23
2.5 序列聚类拼接...........................................................................................................................29
2.5.1 Phrap.............................................................................................................................29
2.5.2 Cap3 ..............................................................................................................................39
2.6 Consed ......................................................................................................................................43
2.7 Primer3 ....................................................................................................................................57
第 3 章 序列的比对 ................................................................................................................................62
3.1 全局比对 ..................................................................................................................................62
3.1.1 Clustalw ...........................................................................................................................62
3.1.2 MUSCLE .........................................................................................................................78
3.1.3 HMMER ..........................................................................................................................81
3.2 局部比对 ..................................................................................................................................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
第 4 章 基因组/基因的注释.................................................................................................................140
4.1 重复序列分析.........................................................................................................................140
4.1.1 RepeatMasker.............................................................................................................140
4.1.2 Trf ..............................................................................................................................151
4.1.3 LTR_STRUC...................................................................................................................155
4.2 RNA分析 ..................................................................................................................................158
4.2.1 tRNAScan.....................................................................................................................158
4.2.2 MicroRNA.....................................................................................................................163
4.2.3 snoRNA.........................................................................................................................171
4.2.4 rRNA（rfam）.............................................................................................................175
4.3 基因预测 ................................................................................................................................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 基因功能注释.........................................................................................................................198
4.4.1 InterproScan.............................................................................................................198
4.4.2 WEGO ............................................................................................................................203
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