RNA sequence secondary structure prediction method based on base fragment coding and ant colony optimization

Abstract

The invention relates to a RNA sequence secondary structure prediction method based on base fragment coding and ant colony optimization, belonging to the field of bioinformatics research. The RNA sequence secondary structure prediction method comprises the steps of: recoding an RNA sequence, and obtaining a corresponding coding sequence according to corresponding values in a coding table and a coding association list; eliminating a redundancy stem region by a strategy of extending rightwards according to an exact matching table and a partial matching table to obtain all possible useable stem region sets; giving two-dimensional heuristic information in the ant colony optimization, selection rule of an initial stem region and the next stem region and updating strategy of pheromones to construct compatible subsets of all possible stem region sets; and finally obtaining a secondary structure with minimum free energy. The invention can rapidly, accurately and effectively predict the secondary structure without including a pseudojnot RNA sequence, can output the obtained result in a bracket mode way, and is superior to the main prediction technology at present in the aspects of sensitivity and specificity of the prediction of the RNA sequence second structure.

Description

technical field [0001] The invention belongs to the field of bioinformatics research. Background technique [0002] Studies have shown that RNA plays a very important role in gene regulation, and the function and structure of RNA are closely related. Therefore, if you want to understand the functional characteristics of RNA sequences, you should start with its structure. At present, a large amount of information on the primary structure of RNA sequences has been obtained, and more and more researchers have begun to pay attention to the secondary and tertiary structures of RNA sequences. However, it is expensive and difficult to determine the tertiary structure by biological experiments. And it doesn't work for all molecules. At the same time, the tertiary structure of RNA sequences is difficult to obtain directly through the primary structure, and the theoretical prediction of its tertiary structure is not going very smoothly. Predicting the secondary structure is the only ...

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Problems solved by technology

At present, a large amount of information on the primary structure of RNA sequences has been obtained, and more and more researchers have begun to pay attention to the secondary and tertiary structures of RNA sequences. However, it is expensive and difficult to determine the tertiary structure by biological experiments. and it doesn't work for all molecules

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