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Corn lncRNA screening and classifying method based on ARM processor

An ARM processor, screening and classification technology, applied in the field of bioinformatics research, can solve the problems of inability to calculate within a reasonable time, without any optimization, and high time complexity, and achieve easy batch processing of data, high accuracy, and high code. The effect of density

Inactive Publication Date: 2018-01-12
JILIN UNIV
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Problems solved by technology

The enumeration method is the easiest method to think of and understand, but this method does not have any optimization, the time complexity is high, and it cannot be calculated in a reasonable time
Therefore, the enumeration method can only be theoretically feasible, and cannot be practically applied in longer sequences

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  • Corn lncRNA screening and classifying method based on ARM processor
  • Corn lncRNA screening and classifying method based on ARM processor

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Embodiment Construction

[0025] The present invention will be further described in detail below in conjunction with the accompanying drawings, so that those skilled in the art can implement it with reference to the description.

[0026] Such as figure 1 , figure 2 As shown, the existing lncRNA screening and classification methods first collect high-throughput lncRNA data according to traditional design rules, and then screen and classify them. The collection of lncRNA needs to be carried out with biological experimental equipment. The current method is not convenient to combine with high-throughput data collection equipment, etc., and the labor cost is high, the speed is slow, and the efficiency is low. Therefore, it is urgent to solidify the lncRNA classification method to high-throughput data In the collecting instrument, optimize lncRNA screening classification; Therefore, the invention provides a kind of corn lncRNA screening classification method based on ARM processor, the required hardware eq...

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Abstract

The invention discloses a corn lncRNA screening and classifying method based on an ARM processor. The method comprises the following steps that firstly, a full-length cDNA sequence of corn is input into a CPLD; secondly, a cDNA sequence with the length larger than 200 is screened out, open reading frame prediction is carried out on cDNA, a threshold is determined, the cDNA with the length smallerthan the threshold is determined, the cDNA is in homologous comparison with known protein, non-homologous parts are reserved, secondary structure prediction is carried out on existing plant lncRNA, secondary structure features are extracted, meanwhile, secondary structure prediction is conducted on remaining sequences, the part meeting the structure features is reserved, the to-be-screened cDNA sequence is compared with the small RNA sequence, and a small RNA precursor is removed; thirdly, the corn lncRNA sequence with the known function is collected, structure prediction is conducted, structure feature extraction and screening are conducted on the functional lncRNA, known functional corn lncRNA structure feature sets are constructed, secondary structure extraction is conducted on the cornlncRNA screened out in the second step, the structure feature sets are compared, and lncRNA functions are confirmed and classified.

Description

technical field [0001] The invention relates to the field of bioinformatics research, in particular to a method for screening and classifying corn lncRNA based on an ARM processor. Background technique [0002] The secondary structure of RNA refers to the stem-loop structure formed by RNA self-folding due to complementary base pairing. Due to complementary base pairing, although RNA is a single strand, it will fold itself in some regions to form a double helix structure, making the three-dimensional structure of RNA complex. In addition to the typical pairing (Waston-Crick pairing, A=U, G≡C), there is the exception of G=U (wobble basepairs swing pairing). G≡C has the highest stability, and G=U has the lowest stability. In the secondary structure, the stem is the place where bases are paired continuously, and it is a double helix region formed according to the pairing rules of A=U, G≡C, and G=U mentioned above. The part of the single strand that does not form a pair is a l...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22
Inventor 张浩刘元宁占萌苹李誌
Owner JILIN UNIV
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