Section: New Results
Co-linear chaining on graphs
We reported the first algorithm that perform co-linear chaining between a sequence and a directed acyclic graph (DAG) [9].
This work concerns dynamic programming algorithms and sequencing alignment.
The problem of co-linear chaining is a classical bioinformatics problem, which has immediate application to sequence alignment, as it is used as a filter remove spurious alignment seeds.
Co-linear chaining is typically solved using a simple dynamic programming algorithm.
Yet, representations of genomes using graphs instead of sequences have recently became an active research topic. As a results, the problem of aligning
a sequence to a sequence graph merits consideration. This work provides the first step towards tackling practical sequence-to-graph alignment instances,
by first considering the case when the graph is a DAG. We designed a