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  • The Inria's Research Teams produce an annual Activity Report presenting their activities and their results of the year. These reports include the team members, the scientific program, the software developed by the team and the new results of the year. The report also describes the grants, contracts and the activities of dissemination and teaching. Finally, the report gives the list of publications of the year.

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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 O(k|E|log|V|) algorithm to solve co-linear chaining on DAGs, which matches the optimal solution for the classical sequence variant, i.e. when the graph is a path.