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. 2007 Jul;35(Web Server issue):W325-9.
doi: 10.1093/nar/gkm303. Epub 2007 May 8.

taveRNA: a web suite for RNA algorithms and applications

Cagri Aksay  1 , Raheleh Salari, Emre Karakoc, Can Alkan, S Cenk Sahinalp
Affiliations

taveRNA: a web suite for RNA algorithms and applications

Cagri Aksay et al. Nucleic Acids Res. 2007 Jul.

Abstract

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.

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Figures

Figure 1.
Figure 1.
The output pages of taveRNA. (a) alteRNA secondary structure prediction for 5sRNA. (b) inteRNA joint structure prediction for CopA and CopT.
See this image and copyright information in PMC

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