Efficient Genome Indexing for Large-Scale Linked Interval Data

Efficiently querying specific genomic regions is fundamental in bioinformatics, which allows to extract relevant feature information from large genomic datasets. While existing tools provide query capabilities, they are limited to interval manipulation and do not natively support linked interval data or complex relationship between genomic features. We introduce genogrove, a hybrid graph data structure designed to facilitate scalable interval queries. We demonstrate how it serves as an efficient interval search structure for large-scale datasets and lays the foundation for more advanced genomic analyses, supporting a wide range of applications in bioinformatics.