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Method for designing microRNA probe sequence

A probe sequence and design method technology, applied in the field of microRNA probe analysis, can solve the problems of inability to use microRNA probe sequence design, limiting the value of microRNA chips, and low accuracy.

Inactive Publication Date: 2011-02-23
NANJING UNIV
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Problems solved by technology

Including a study based on SVM (document 4: Reliable prediction of Drosha processing sites improvesmicroRNA gene prediction, S.A.Helvik, O. Jr and Pal Saetrom, BIOINFORMATICS, 23(2), 2007, p142-149), this method can only predict the position of one end of people's microRNA in its precursor stem-loop structure (that is, this method can only give accurate microRNA Precursor, namely pre-microRNA), and cannot provide a complete and accurate nucleic acid sequence of the mature microRNA; the other two are based on Hidden Markov chain and Bayesian formula, but the accuracy is too low to be used for microRNA probes sequence design
Limits the value of microRNA chips in practical applications

Method used

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  • Method for designing microRNA probe sequence
  • Method for designing microRNA probe sequence
  • Method for designing microRNA probe sequence

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Embodiment Construction

[0040] Such as figure 1 As shown, the chip probes are designed according to the detection requirements according to the database and the calculation method to analyze the microRNA mature body sequence, and the internal standard and external standard probes are designed; the probes are synthesized on the substrate or the probes are synthesized and then spotted with a spotter Fixed on the substrate of the chip; after fluorescently labeling the sample to be tested, the sample is added to the high-throughput biochip detection device, hybridized with the microRNA probe on the chip, and cleaned to remove impurities after hybridization; photoelectric detection, such as Fluorescence signal image scanning, recording microRNA expression intensity data, and preprocessing the data to generate microRNA expression profile data.

[0041] The method of the embodiment of the present invention is specifically as follows figure 2 Shown:

[0042] Step 1. Input the nucleic acid sequence of the genome,...

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Abstract

The invention discloses a method for designing a microRNA probe sequence. The method comprises the following steps of: collecting all stem seed sequences which can form a stem-loop structure from a genome sequence; calculating RNA secondary structures formed by each stem seed sequence and sequences in an area within 100 to 150nt close to the stem seed sequences; screening the generated RNA secondary structures according to the characteristics of a pre-microRNA stem-loop structure to extract a microRNA-containing stem-loop structure; calculating the free energy distribution of the microRNA-containing stem-loop structure; determining a pre-microRNA by using a free energy characteristic spectrum of the microRNA stem-loop structure; converting the pre-microRNA secondary structure into an equivalent length of a mature body by using a standard transformational relation; and intercepting a microRNA mature body sequence from the pre-microRNA secondary structure by using a set equivalent totallength and outputting a result.

Description

Technical field [0001] The invention relates to the technical field of a high-flux microRNA chip, in particular to an analysis method of a microRNA probe. Background technique [0002] High-throughput biochip technology is an advanced technology that integrates microelectronics, molecular biology, computer science and other disciplines. It can integrate thousands to tens of thousands of molecular probes on a centimeter-sized computer chip to achieve various processes in the organism. , Each state performs rapid, parallel, and large-information detection at all levels. Among them, microRNA chip technology is the latest chip technology, and its probe is a new RNA molecule called microRNA. This type of RNA molecule regulates gene expression by inhibiting the translation of mRNA or degrading mRNA. In the past decade, a large number of studies have proved that microRNA is widely involved in the growth and development of animals and plants, cell differentiation and apoptosis, and the ...

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Application Information

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IPC IPC(8): C12N15/10
Inventor 王进何沉峰李颖新杨嵘严先昭龚晨光李捷周志华张辰宇
Owner NANJING UNIV
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