McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data

Alternative splicing removes intronic sequences from pre-mRNAs in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts gives specific functionalities to cells in a particular condition or developmental stage. In addition, a large fraction of human disease mutations affect splicing and lead to aberrant mRNA and protein products. Current methods that interrogate the transcriptome based on RNA-seq either suffer from short read length when trying to infer full-length transcripts, or are restricted to predefined units of alternative splicing that they quantify from local read evidence.