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Nucleic Acids Research 2005 33(Web Server Issue):W570-W572; doi:10.1093/nar/gki379
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

dnaMATE: a consensus melting temperature prediction server for short DNA sequences

Alejandro Panjkovich, Tomás Norambuena and Francisco Melo*

Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile Alameda 340, Santiago, Chile

*To whom correspondence should be addressed. Tel: +56 2 686 2279; Fax: +56 2 222 55 15; Email: fmelo{at}bio.puc.cl

Received February 7, 2005. Revised March 8, 2005. Accepted March 8, 2005.

An accurate and robust large-scale melting temperature prediction server for short DNA sequences is dispatched. The server calculates a consensus melting temperature value using the nearest-neighbor model based on three independent thermodynamic data tables. The consensus method gives an accurate prediction of melting temperature, as it has been recently demonstrated in a benchmark performed using all available experimental data for DNA sequences within the length range of 16–30 nt. This constitutes the first web server that has been implemented to perform a large-scale calculation of melting temperatures in real time (up to 5000 DNA sequences can be submitted in a single run). The expected accuracy of calculations carried out by this server in the range of 50–600 mM monovalent salt concentration is that 89% of the melting temperature predictions will have an error or deviation of <5°C from experimental data. The server can be freely accessed at http://dna.bio.puc.cl/tm.html. The standalone executable versions of this software for LINUX, Macintosh and Windows platforms are also freely available at the same web site. Detailed further information supporting this server is available at the same web site referenced above.


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