Method for predicting secondary structure of ribonucleic acid (RNA) sequence based on complex programmable logic device (CPLD) base fragment encoding and ant colony algorithm

Abstract

The invention discloses a method for predicting a secondary structure of a ribonucleic acid (RNA) sequence based on complex programmable logic device (CPLD) base fragment encoding and ant colony algorithm and belongs to the field of bioinformatics research. The method comprises the following steps: recoding the RNA sequence according to an association table by using the CPLD; obtaining a corresponding encoding sequence according to corresponding value in an encoding table and an encoded association table, removing a redundancy stem area through a right extension strategy through a complete matching table and an incomplete matching table, and obtaining all possible stem area sets; giving two-dimensional heuristic information and a selection rule of an initial stem area and the next stem area in the ant colony algorithm, and constructing a compatible subset of all the possible stem area sets through an information element update strategy; and finally, obtaining the secondary structure with the minimum free energy. The method can rapidly, accurately and effectively predict the secondary structure of the RNA sequence which does not contain false knots and output the obtained result in a bracketing mode, has sensitivity and specificity in the aspect of judging two parameters for predicting the advantages and weakness of the secondary structure of the RNA sequence, and is superior to the conventional mainstream prediction technology.

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, but the useful information contained in the primary structure is relatively small. Therefore, more and more researchers have begun to pay attention to the secondary and tertiary structures of RNA sequences. It is expensive and difficult to determine the tertiary structure of RNA, and this method is not effective for all molecules. Since the tertiary structure of RNA sequences is difficult to obtain directly through the primary structure, and the theoretical prediction directly oriented to the tertiary stru...

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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, but the useful information contained in the primary structure is relatively small. Therefore, more and more researchers have begun to pay attention to the secondary and tertiary structures of RNA sequences. It is expensive and difficult to determine the tertiary structure of RNA, and this method is not effective for all molecules

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