Alignment-free methods for detecting gene fusions in long-read transcriptomes

• Grant number: 24/14925-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: November 01, 2024
• End date: July 31, 2025
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Theory of Computation
• Principal Investigator: João Meidanis
• Grantee: Luísa de Melo Barros Penze
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

Methods based on the notion of minimal absent words have been used to compare genomes in an alignment-free manner and to detect structural variants in genomes, both using Whole Genome Sequencing (WGS) data from long reads. Since this approach offers several advantages over alignment-based methods, it is expected that the implementation of algorithms based on the concept of minimal absent words for the detection of gene fusions will involve a significant improvement in performing such a task. Thus, the objective of this project is to study the necessary adaptations to apply these alignment-free methods to detect fusions in RNA data, also from long reads. Additionally, this new approach is intended to be compared with state-of-the-art methods for gene fusion detection in long reads.