miRanda打分原理

report

miranda算法

miranda的基本算法，主要是根据两个方法：

1. 与miRNA成熟体seed序列的匹配程度，匹配程度越高，打分越高；
2. miRNA成熟体与target之前的相匹配的热力学能量值，能量值越低，说明miRNA成熟体与target的结合就越稳定；

基于miranda/targetscan/RNAhybrid预测的target进行过滤

一般来说，只依赖于计算生物学的方法预测靶标位点的准确性不是太高，所以要利用其它的feature进行过滤。

1. miRanda-predicted miRNA::site duplex. Duplex features include a bit representation of base-pairing at the seed region and the extent of 3' binding.
2. the local context of the candidate site. Local features include AU composition flanking the target site and secondary structure accessibility score.
3. the global context of the site in the 3' UTR. Global features include length of UTR, relative position of target site from UTR ends, and conservation level of the block containing the target site.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-8-r90

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2003-5-1-r1