The major scientific new direction of this project is to study what happens to selected classical sequence analysis tasks when labeled directed acyclic graphs (labeled DAGs) are used as inputs.

The Academy of Finland granted Mäkinen's Genome-scale algorithmics research group a 4-year project "Sequence analysis revisited and extended".

The project studies implications of bidirectional Burrows-Wheeler transform -based techniques to sequence analysis and widens the scope of such analyses to labeled directed acyclic graphs (labeled DAGs). The motivation for these new directions come from several timely applications in genome research, e.g., in new ways to  represent diploid genomes and pan-genomes in place of the commonly adopted use of a single sequence as the basis of analyses.

For some new results obtained after submission of the plan, see our research themes space-efficient sequence analysis, transcript assembly, and recombination-aware sequence alignment.