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Hidden Markov Models applied to transposable elements

Grant number: 12/24774-2
Support Opportunities:Scholarships abroad - Research
Start date: March 15, 2013
End date: July 14, 2013
Field of knowledge:Physical Sciences and Mathematics - Computer Science
Principal Investigator:Carlos Norberto Fischer
Grantee:Carlos Norberto Fischer
Host Investigator: Marie-France Sagot
Host Institution: Instituto de Geociências e Ciências Exatas (IGCE). Universidade Estadual Paulista (UNESP). Campus de Rio Claro. Rio Claro , SP, Brazil
Institution abroad: Université Claude Bernard Lyon 1, France  

Abstract

Transposable Elements are stretches of DNA that can "move" from a site to another in a genome. Hidden Markov Models have been used in the solution of some problems of the Molecular Biology. In this project, Hidden Markov Models will be applied to the identification and classification of Transposable Elements. The project will be developed in the Research Group Bamboo, of INRIA, that belongs to the Laboratory of Biometry and Evolutionary Biology at the University of Lyon 1, France, that works on Bioinformatics and Computational Biology. It is expected that collaborative projects can be proposed in the future between the Group of Bioinformatics of Rio Claro and the Bamboo Group. (AU)

News published in Agência FAPESP Newsletter about the scholarship:
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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, . (11/00428-5, 12/22205-0, 12/24774-2)
SCHIETGAT, LEANDER; VENS, CELINE; CERRI, RICARDO; FISCHER, CARLOS N.; COSTA, EDUARDO; RAMON, JAN; CARARETO, CLAUDIA M. A.; BLOCKEEL, HENDRIK. A machine learning based framework to identify and classify long terminal repeat retrotransposons. PLOS COMPUTATIONAL BIOLOGY, v. 14, n. 4, . (15/14300-1, 13/15070-4, 12/24774-2)
FISCHER, CARLOS N.; CARARETO, CLAUDIA M. A.; DOS SANTOS, RENATO A. C.; CERRI, RICARDO; COSTA, EDUARDO; SCHIETGAT, LEANDER; VENS, CELINE. Learning HMMs for nucleotide sequences from amino acid alignments. Bioinformatics, v. 31, n. 11, p. 1836-1838, . (12/24774-2, 10/10731-4)