In collaboration with Prof. K. Park and Dr. S. Park, from the Seoul National University, in Southern Korea, we propose a new, efficient algorithm to build the Hierarchical Overlap Graph (HOG). This graph stores succinctly the ways overlapping reads can be merged to build superstrings.
The article has been accepted for publication at SPIRE 2020 (see https://www.cs.ucf.edu/spire2020/index.php/accepted-papers/).
The boom of genomic sequencing makes compression of sets of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the …
Discovering DNA binding sites in genome sequences is crucial for understanding genomic regulation. Currently available computational tools for finding binding sites with Position Weight Matrices of known motifs are often used in restricted genomic …
With the increasing impact of genomics in life sciences, the inference of high quality, reliable, and complete genome sequences is becoming critical. Genome assembly remains a major bottleneck in bioinformatics: indeed, high throughput sequencing …
Covering a directed graph by a Hamiltonian path or a set of words by a superstring belong to well studied optimisation problems that prove difficult to approximate. Indeed, the Maximum Asymmetric Travelling Salesman Problem (Max-ATSP), which asks for …