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Hidden Markov Models for the Identification of Conserved Domains of Transposable Elements (LTR-Retroelements)

Grant number: 14/14589-9
Support type:Scholarships in Brazil - Scientific Initiation
Effective date (Start): September 01, 2014
Effective date (End): August 31, 2015
Field of knowledge:Physical Sciences and Mathematics - Computer Science - Computer Systems
Principal Investigator:Carlos Norberto Fischer
Grantee:Mariana Fantini
Home Institution: Instituto de Geociências e Ciências Exatas (IGCE). Universidade Estadual Paulista (UNESP). Campus de Rio Claro. Rio Claro , SP, Brazil


The Group of Bioinformatics of Rio Claro developed a computational system, called SATEComp, aimed at helping the annotation of Transposable Elements (TEs) in genome sequences. The SATEComp uses the homology method and Hidden Markov Models (HMMs), providing comparative results between these two ways of TE identification. Two other projects (2012 and 2014) proposed five alternative ways to obtain the representative sequences of TEs used to produce the necessary alignments to train HMMs. In this project, the student will work on new alternatives to try to improve the results obtained specifically considering the use of HMMs. She will study topics related to TEs and HMMs aiming at implementing alternatives to obtain the representative sequences of TEs for training for the identification and classification of these elements.