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Authors: Giulia Menconi 1 ; Giovanni Battaglia 2 ; Roberto Grossi 2 ; Nadia Pisanti 2 and Roberto Marangoni 2

Affiliations: 1 Istituto Nazionale di Alta Matematica, Italy ; 2 Università di Pisa, Italy

Keyword(s): Residentome, Retrotransposons, Mobile DNA elements, L-grams.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Sequence Analysis

Abstract: We aim at finding all the mobile elements in a genome and understanding their dynamic behavior. Comparative genomics of closely related organisms can provide the data for this kind of investigation. The comparison task requires a huge amount of computational resources, which in our approach we alleviate by exploiting the high similarity between homologous chromosomes of different strains of the same species. Our case study is for RefSeq and two other strains of S. cerevisiæ. Our fast algorithm, called REGENDER, is driven by data analysis. We found that almost all the chromosomes are composed by resident genome (more than 90% is conserved). Most importantly, the inspection of the non-conserved regions revealed that these are putative mobile elements, thus confirming that our method is useful to quickly find mobile elements. The software tool REGENDER is available online at http://www.di.unipi.it/gbattag/regender.

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Paper citation in several formats:
Menconi, G.; Battaglia, G.; Grossi, R.; Pisanti, N. and Marangoni, R. (2011). INFERRING MOBILE ELEMENTS IN S. CEREVISIAE STRAINS. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS; ISBN 978-989-8425-36-2; ISSN 2184-4305, SciTePress, pages 131-136. DOI: 10.5220/0003137001310136

@conference{bioinformatics11,
author={Giulia Menconi. and Giovanni Battaglia. and Roberto Grossi. and Nadia Pisanti. and Roberto Marangoni.},
title={INFERRING MOBILE ELEMENTS IN S. CEREVISIAE STRAINS},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS},
year={2011},
pages={131-136},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003137001310136},
isbn={978-989-8425-36-2},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS
TI - INFERRING MOBILE ELEMENTS IN S. CEREVISIAE STRAINS
SN - 978-989-8425-36-2
IS - 2184-4305
AU - Menconi, G.
AU - Battaglia, G.
AU - Grossi, R.
AU - Pisanti, N.
AU - Marangoni, R.
PY - 2011
SP - 131
EP - 136
DO - 10.5220/0003137001310136
PB - SciTePress

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