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Using long fragments to reconstruct RNA backbones

Tapani Utriainen (Institutionen för data- och informationsteknik, Datavetenskap, Algoritmer (Chalmers) ; Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)) ; Graham J.L. Kemp (Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers))
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering p. 1424-1428. (2007)
[Konferensbidrag, refereegranskat]

This study addresses to what extent RNA backbones consist of long, recurring fragments. A dynamic programming algorithm is presented that finds the smallest set of fragments that are required to reconstruct the backbone of a known macromolecule within a given root mean square bound. This algorithm is guaranteed to find a global minimum. The program has been used for reconstructing the backbones of several known RNA structures, using fragments taken from ribosomal RNA. Each of these target structures could be approximated within a root mean square deviation of 1.0Å using fragments with an average length of more than eight nucleotides.

Denna post skapades 2007-12-14. Senast ändrad 2013-05-29.
CPL Pubid: 63152


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