INFERRING MOBILE ELEMENTS IN S. CEREVISIAE STRAINS

Giulia Menconi, Giovanni Battaglia, Roberto Grossi, Nadia Pisanti, Roberto Marangoni

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.

References

  1. Cohen, J. D. (1997). Recursive hashing functions for ngrams. ACM Trans. Inf. Syst., 15(3):291-320.
  2. Conti, V., Aghaie, A., Cilli, M., and et al. (2006). crv4, a mouse model for human ataxia associated with kyphoscoliosis caused by an mrna splicing mutation of the metabotropic glutamate receptor 1 (grm1). Int. J. Molec. Med., 18:593-600.
  3. Le Rouzic, A., Boutin, T. S., and Capy, P. (2007). Long term evolution of transposable elements. PNAS, 104:19375-19380.
  4. Lewin, B. (2007). Genes (IX ed.). Jones and Bartlett.
  5. Liti, G., Carter, D. M., Moses, A. M., and et al. (2009). Population genomics of domestic and wild yeast. Nature, 458:337-341.
  6. Ohlebusch, E. and Abouelhoda, M. (2006). Chaining algorithms and applications in comparative genomics. Handbook of Computational Molecular Biology.
  7. SGD (2010). SGD project. Saccharomyces Genome Database. http://www.yeastgenome.org.
  8. Venner, S., Feschotte, C., and Biemont, C. (2009). Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet., 25:317-323.
  9. Vigna, S. (2006). fastutil: Fast and compact type-specific collections for java. http://fastutil.dsi.unimi.it.
Download


Paper Citation


in Harvard Style

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 - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 131-136. DOI: 10.5220/0003137001310136


in Bibtex Style

@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 - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={131-136},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003137001310136},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - INFERRING MOBILE ELEMENTS IN S. CEREVISIAE STRAINS
SN - 978-989-8425-36-2
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