Rank distance extensions and counting of sorting scenarios

• Grant number: 20/00740-8
• Support Opportunities: Scholarships in Brazil - Master
• Start date: November 01, 2020
• End date: October 31, 2022
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Theory of Computation
• Principal Investigator: João Meidanis
• Grantee: Lucas Peres Oliveira
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

Advances in DNA sequencing technologies have enabled easy acquisition of genomes in computational environments. Methods for reconstructing phylogenies based on rearrangement events depend on a biologically meaningful notion of distance between genomes that can be computed efficiently. Several distance models and metrics have been developed over the years to achieve these goals, among which matrix modeling and the rank distance have opened a new perspective for the problem. In this work, we intend to consolidate recent advances extending this model to genomes with indels and counting the sorting scenarios that occur between two genomes. Besides, we aim to begin the study of an extension to the rank distance to accommodate genomes with repeated segments. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

PEREIRA ZANETTI, JOAO PAULO; OLIVEIRA, LUCAS PERES; CHINDELEVITCH, LEONID; MEIDANIS, JOAO. Generalizations of the genomic rank distance to indels. Bioinformatics, v. 39, n. 3, p. 10-pg., 2023-03-01. (17/02748-3, 20/00740-8, 18/00031-7)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

OLIVEIRA, Lucas Peres. Extensões e aplicações da distância de posto genômica. 2022. Master's Dissertation - Universidade Estadual de Campinas (UNICAMP). Instituto de Computação Campinas, SP.