| DNA is a carrier of inherited information, the effect of inherited information is carried off by proteinic function , but DNA is not direct stencil of proteinic synthesization, the stencil of proteinic synthesization is RNA . The prediction of RNA secondary structure is used in the functional analysis of the protein. The RNA secondary prediction is one of the basic subjects for the computer science and biological science , thermodynamics minimal free energy method and the methods of sequence contrastive analysis are the two basic methods to predict RNA secondary structure. The idea of sequence contrastive analysis is finding the comparability of the detected sequences and the goal sequences, the final realization of sequence contrast must depend on the mathmatics model. The sequence contrastive analysis can not be applied between the similar sequence and new independent sequence .The most algorithms of predicing RNA secondary structure can only predict nested RNA secondary structure, pseudoknot is not permitted in it . but pseudoknot has important function in RNA , for example: Pleij and his colleagues had predicted successfully structure containing pseudoknot in RnaSe P RNAS in 1985, and approved by Kock and his colleagues in 1998.The problem for predicting RNA secondary structure containing pseudoknots is NP-complete. Now several dynaming programmings for predicting RNA secondary structure containing pseudoknots are given: Rivas algorithm, Lyngs Φ algorithm and the algebra dynamic programmin algorithm and so on. Rivas algorithm and Lyngs Φ algorithm have become the common method selected to predict RNA secondary structure containing pseudoknots , and the algebra dynamic programming are the better as we know to predict RNAsecondary structure containing pseudoknots. Rivas algorithm can compute random planar pseudoknots and non-planar pseudoknots containing a special condition, and its time complexity is 0 (n6) and its space complexity is0 (n4) . Lyngs |
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