taveRNA: a web suite for RNA algorithms and applications

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.

• Type: Journal
• Year: 2007
• Where: NAR
• Authors: Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp
• Keywords: Dynamic Programming, NAR 2007, Rna Secondary Structure, Structure Prediction