Suffix arrays and genome assembly

• Grant number: 13/01752-6
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Start date: April 01, 2013
• End date: June 30, 2013
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
• Principal Investigator: Cristina Dutra de Aguiar
• Grantee: Felipe Alves da Louza
• Supervisor: Steve Hoffmann
• Host Institution: Instituto de Ciências Matemáticas e de Computação (ICMC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Institution abroad: Leipzig University, Germany
• Associated to the scholarship: 11/15423-9 - Development of a persistent biological index based on generalized suffix arrays, BP.MS

Abstract

The master project conducted by the candidate deals with algorithms to construct and query suffix arrays in external memory. Suffix arrays have been used in different tasks in bioinformatics. Recently Simpson and Durbin (2012) used suffix arrays to assembly genomes efficiently. However, the internal memory requirements impair their usage in large datasets. The objective of the proposed internship project is to investigate genome assembling using the suffix arrays in external memory, with a special focus on how to efficiently detect and deal with genomic repeats. (AU)