A polynomial delay algorithm for the enumeration of bubbles with length
constraints in directed graphs and its application to the detection of
alternative splicing in RNA-seq data
We present a new algorithm for enumerating bubbles with length constraints in
directed graphs. This problem arises in transcriptomics, where the question is
to identify all alternative splicing events present in a sample of mRNAs
sequenced by RNA-seq. This is the first polynomial-delay algorithm for this
problem and we show that in practice, it is faster than previous approaches.
This enables us to deal with larger instances and therefore to discover novel
alternative splicing events, especially long ones, that were previously
overseen using existing methods.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013