The full text of this article

 

Extended shapes for the combinatorial design of RNA sequences
by Marc Hellmuth, Daniel Merkle, Martin Middendorf
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 2, No. 4, 2009

 

Abstract: It is known that for two given secondary structures (defined by position of base pairings) an RNA string can easily be found that can fold into both structures. For more than two secondary structures this is not necessarily possible. In this paper, we introduce pseudo edges that are used to forbid that certain base pairs can bind and therefore can be used to define the properties of possible RNA secondary structures. We study the complexity of the problem to design an RNA sequence that can fold into different secondary structures each of them is described by a set of required and forbidden base pairs. We refine the NP-completeness results of Clote et al. (2005) and show an analogous NP-completeness result for the realisation problem concerning the removal of (pseudo) edges. We also present a polynomial time method for checking the realisability of extended shape graphs. Furthermore, we empirically analyse the influence of pseudo edges on the realisability for sets of random RNA sequences and for sets of aptamers.

Online publication date: Mon, 04-Jan-2010

 

is only available to individual subscribers or to users at subscribing institutions.

 
Existing subscribers:
Go to Inderscience Online Journals to access the Full Text of this article.

 
Pay per view:
If you are not a subscriber and you just want to read the full contents of this article, buy online access here.

 
Complimentary Subscribers, Editors or Members of the Editorial Board of the International Journal of Computational Biology and Drug Design (IJCBDD):
Login with your Inderscience username and password:

 

    Username:        Password:         

Forgotten your password?


 
Want to subscribe?
A subscription gives you complete access to all articles in the current issue, as well as to all articles in the previous three years (where applicable). See our Orders page to subscribe.

 
If you still need assistance, please email subs@inderscience.com