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Bioinformatics Advance Access published online on June 9, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn259
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DNAlive: A tool for the physical analysis of DNA at the genomic scale

J.Ramon Goñi 1, Carlos Fenollosa 1,2, Alberto Pérez 1,2,3, David Torrents 1,4 and Modesto Orozco 1,2,3,*

1Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028. Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Barcelona 08034, Spain
2National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
3Departament de Bioquímica, Facultat de Biología, Avgda Diagonal 647, Barcelona 08028, Spain
4Institut Català per la Recerca i Estudis Avançats (ICREA). Barcelona Spain.

*To whom correspondence should be addressed. Dr. Modesto Orozco, E-mail: modesto{at}mmb.pcb.ub.es


  Abstract

Summary: DNAlive is a tool for the analysis and graphical display of structural and physical characteristics of genomic DNA. The web server implements a wide repertoire of metrics to derive physical information from DNA sequences with a powerful interface to derive three-dimensional information on large sequences of both naked and protein-bound DNAs. Furthermore, it implements a mesoscopic Metropolis code which allows the inexpensive study of the dynamic properties of chromatin fibers. In addition, our server also surveys other protein and genomic databases allowing the user to combine and explore the physical properties of selected DNA in the context of functional features annotated on those regions.

Availability: http://mmb.pcb.ub.es/DNAlive/ ; http://www.inab.org/

Contact: modesto{at}mmb.pcb.ub.es

Supplementary information:

Associate Editor: Prof. Alfonso Valencia

Received on March 27, 2008; revised on May 16, 2008; accepted on June 4, 2008

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