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

TL;DR

This paper introduces the first polynomial-delay algorithm for enumerating length-constrained bubbles in directed graphs, significantly improving the detection of complex alternative splicing events in RNA-seq data.

Contribution

It presents a novel polynomial-delay enumeration algorithm for bubbles with length constraints, enhancing the analysis of alternative splicing in transcriptomics.

Findings

Algorithm is faster than previous methods in practice.

Enables discovery of longer, previously overlooked splicing events.

Handles larger instances effectively.

Abstract

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.