1 RNA分子的功能多样性

ncRNA非编码RNA

1. "Ancient" housekeeping ncRNAs and the RNA world hypothesis
2. "Young" ncRNAs as regulatory layer in complex organisms

2、RNA转录重建

a) Map to Genome Methods: (e.g. Tuxedo suite and Cufflinks)
Individual reads. Spliced reads. Transcript abundance

1. 将未剪接的reads比对到基因组(Bowtie- Burrows-Wheelr快速短读比对-候选外显子中心+潜在剪接位点
2. 对齐拼接reads(TopHat)-使用标记的拼接站点对齐拼接短读
3. 转录本重建(Cuffdiff)
4. 差异表达分析(Cuffdiff)-转录数的概率分配
5. 可视化和分析(CummeRbund-询问和解决生物学问题的应用程序

b) Align-de-novo approaches (e.g. Trinity)
-> Linear contigs.
Group contigs.
Transcript resolving.

c) Differential expression analysis
-> Variability: Technical, biological, uncertainty.

3、RNA折叠

RNA 二级结构指由非相邻碱基相互作用折叠形成的平面结构。Nussinov 算法是最早使用动态规划进行 RNA 二级结构预测的算法,但算法的预测精度却不高。