Rearrangement distances in unbalanced genomes considering intergenic regions

• Grant number: 22/13555-0
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: March 01, 2023
• End date: February 29, 2024
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Theory of Computation
• Principal Investigator: Zanoni Dias
• Grantee: Gabriel Henriques Siqueira
• Supervisor: Guillaume Fertin
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Institution abroad: Université de Nantes, France
• Associated to the scholarship: 21/13824-8 - Generalization of string partition problems, BP.DR

Abstract

Rearrangement Distance problems are computational problems inspired by biology with many variations that have been studied over time. These problems consist in finding the minimum sequence of rearrangement events, which are large scale mutations, necessary to transform one genome into another. Originally, rearrangement distance problems considered only the gene sequence and assumed that each gene has only one copy in the genome. More recent studies have been incorporating information regarding intergenic regions, which are structures present between genes and in the extremes of the genome, and start to assume that genes can have multiple copies. This project focuses on rearrangement distances that consider two rearrangement events, the reversal, which inverts a sequence of genes, and the transposition, which exchanges two adjacent sequences of genes. Our study will focus on a genome representation that allows for multiple copies of each gene and includes information about intergenic regions. We consider one representation where each intergenic region is encoded by the number of nucleotides in it, and a more flexible representation were the number of nucleotides in an intergenic region must belong to an interval. The more flexible representation accounts for alterations cause by local small scale mutations and errors in the genome sequencing. (AU)