外显子剪接过程
The whole process is regulated by trans-acting elements such as SR proteins, heterogeneous nuclear ribonucleoproteins, and the regulatory complex. ESE, exonic splicing enhancer; ESS, exonic splicing silencer; ISE, intronic splicing enhancer; ISS, intronic splicing silencer; ss, splice site.
文章解读
In silico prediction of splice-altering single nucleotide variants in the human genome
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267638/
拼接机制：
(i) splicing signals, including the 5′/3′ splice site and the branch point;
(ii) splicing regulatory elements, i.e. exonic/intronic splicing enhancers/silencers;
(iii) the spliceosome and other trans-acting elements that bind to cis-acting elements.
结论：
提出两种集成学习方法，自适应增强（AdaBoost）和随机森林，被用于构建改进预测的新模型。
预先计算了人类基因组中所有潜在scSNV的整体评分，并将这两个分数及其相应的注释信息作成数据库（dbscSNV）
dbscSNV数据库（推荐使用）
以chr22的vcf测试
annovar注释结果筛选值大于0.6的：
dbscsnv11 0.9833 22 19950045 19950045 T A het 116.77 22
dbscsnv11 0.9465 22 22049783 22049783 C T het 151.77 14
对于内含子内部的位点，目前软件很难预测准确，当怀疑为内含子突变引起的可变剪切时，也许可做一个RNA逆转录。
其他在线识别剪接工具
GeneSplicer
http://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml
HumanSplicingFinder
http://www.umd.be/HSF/
NetGene2
http://www.cbs.dtu.dk/services/NetGene2
NNSplice
http://www.fruitfly.org/seq_tools/splice.html
FSPLICE
http://www.softberry.com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind
Augustus
http://bioinf.uni-greifswald.de/augustus/submission.php
SPANR：
http://tools.genes.toronto.edu
HSF3：
http://umd.be/HSF3/
补充文章：InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294755/
InterVar：2015年ACMG-AMP指南对遗传变异的临床解释
对用ANNOVAR生成突变注释信息进行了解释并有特定的打分，最后归为五层分类系统
ACMG和AMP以来自不同数据共28个标准，推荐遗传变异使用五层分类系统：pathogenic, likely pathogenic, uncertain significance, likely benign, and benign
