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Nucleic Acids Research Advance Access originally published online on May 8, 2007
Nucleic Acids Research 2007 35(Web Server issue):W325-W329; doi:10.1093/nar/gkm303
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W325-W329
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

taveRNA: a web suite for RNA algorithms and applications

Cagri Aksay1, Raheleh Salari1, Emre Karakoc1, Can Alkan2 and S. Cenk Sahinalp1,*

1Lab for Computational Biology, SFU, Canada and 2Department of Genome Sciences, University of Washington

*To whom correspondence should be addressed. Tel: +1-604-268-7040; Fax: +1-604-291-3045; Email: cenk{at}cs.sfu.ca

Received January 31, 2007. Revised April 3, 2007. Accepted April 14, 2007.

We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic programming solution that minimizes the sum of energy density and free energy of an RNA structure. inteRNA is the first RNA–RNA interaction structure prediction web service. It also employs a dynamic programming algorithm to minimize the free energy of the resulting joint structure of the two interacting RNAs. Lastly, pRuNA is an efficient database pruning service; which given a query RNA, eliminates a significant portion of an ncRNA database and returns only a few ncRNAs as potential regulators. taveRNA is available at http://compbio.cs.sfu.ca/taverna.

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.


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