Hidden Markov models applied to transposable elements

• Grant number: 12/22205-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: February 01, 2013
• End date: January 31, 2014
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computer Systems
• Principal Investigator: Carlos Norberto Fischer
• Grantee: Victor de Abreu Campos
• Host Institution: Instituto de Geociências e Ciências Exatas (IGCE). Universidade Estadual Paulista (UNESP). Campus de Rio Claro. Rio Claro , SP, Brazil

Abstract

SATE Comp is a computational system aimed to help in the analysis processes of Transposable Elements (TEs). The system can identify and classify TEs in genomic sequences utilizing the homology process (using the Repeat Masker application) and Hidden Markov Models (HMMs) (using the HMMER application). In this project, the student will search for ways of improving the results obtained nowadays by SATE Comp, more specifically the results produced using HMMs. For this, the student will study topics related to TEs and HMMs in order to find alternatives to generate the necessary HMMs for the identification and classification of TEs.(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)

FISCHER, CARLOS N.; CAMPOS, VICTOR DE A.; BARELLA, VICTOR H.. On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models. JOURNAL OF COMPUTATIONAL BIOLOGY, v. 25, n. 5, p. 517-527, MAY 2018. (11/00428-5, 12/22205-0, 12/24774-2)