Work

Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length

Year: 2020

Type: article

Abstract: Universal hitting sets (UHS) are sets of words that are unavoidable: every long enough sequence is hit by the set (i.e., it contains a word from the set). There is a tight relationship between UHS and minimizer schemes, where minimizer schemes with low density (i.e., efficient schemes) correspond to UHS of small size. Local schemes are a generalization of minimizer schemes that can be used as replacement for minimizer scheme with the possibility of being much more efficient. We establish the link between efficient local schemes and the minimum length of a string that must be hit by a UHS. We give bounds for the remaining path length of the Mykkeltveit UHS. In addition, we create a local scheme with the lowest known density that is only a log factor away from the theoretical lower bound.

Source: Journal of Computational Biology

DOI: 10.1089/cmb.2020.0432

Authors: Hongyu Zheng, Carl Kingsford, Guillaume Marçais

Institution: Carnegie Mellon University

Language: English

Topic: Algorithms and Data Compression

Subfield: Theoretical Computer Science

Field: Mathematics

Domain: Physical Sciences

Open Access status: hybrid

Funders: National Science Foundation, Gordon and Betty Moore Foundation, National Institutes of Health, National Institute of General Medical Sciences

Awards: Data Discovery: Computational Methods for Searching Short-Read Sequencing Experiments, AF: Small: Multiscale Spectral Signatures for Local and Multi-objective Biological Network Alignment, Carl Kingsford Investigator Award, CAREER: Model-based Reconstruction of Ancient Biological Networks, G3701251748