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A method for target gene prediction in microRNA coding region

A coding region and target gene technology, applied in special data processing applications, instruments, electrical digital data processing, etc.

Inactive Publication Date: 2011-12-07
SHANGHAI CLUSTER BIOTECH
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Problems solved by technology

[0008] However, most of the current microRNA prediction algorithms and software are based on the view that the binding sites of microRNA and target genes are all in the 3'-UTR of the gene. In fact, a series of articles published in late 2008 showed that the binding sites of microRNA and target genes dots may also be in gene coding regions

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  • A method for target gene prediction in microRNA coding region
  • A method for target gene prediction in microRNA coding region
  • A method for target gene prediction in microRNA coding region

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Embodiment Construction

[0025] We take the target gene prediction of the planarian coding region as an example to illustrate the implementation process of the method of the present invention:

[0026] (1) Establish a coding region sequence database

[0027] The mRNA sequence of Schmidteamediterranea was downloaded from http: / / www.ncbi.nlm.nih.gov. By writing a PERL script program to obtain the coding sequence of the protein from the mRNA sequence, a coding region sequence database was established.

[0028] (2) Align the coding region sequences in mammals to find conserved segments.

[0029] Using the online BLAST program (http: / / www.ncbi.nlm.nih.gov / blast) to compare the sequences of mammalian coding regions, remove the poorly conserved coding region sequences, and proceed to the next step.

[0030] (3) Obtain the sequence information of planarian microRNA

[0031] Download all known mature microRNA sequences of planarians from http: / / microrna.sanger.ac.uk / sequences /

[0032] (4) Prediction of ta...

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Abstract

The invention relates to a method for predicting a microRNA target gene, which is suitable for predicting the target gene of the microRNA located in the gene coding region. The present invention includes the following procedures: step 1, establishing the coding region sequence database of the organism to be studied; step 2, performing sequence comparison with the coding region sequences of other species to find conserved segments; step 3, designing a target gene prediction program and compiling and debugging; step 4, for each microRNA, scan the coding regions of all genes, and obtain binding sites from conserved sequences; step 5, statistics and query of target genes; step 6, experimental verification. The method has the advantages of simple implementation, high reliability of results, and can meet the needs of prediction of target genes in most microRNA coding regions.

Description

technical field [0001] The invention belongs to the field of biotechnology, and relates to a method for predicting microRNA target genes, which is applicable to the prediction of microRNA target genes located in gene coding regions. Background technique [0002] MicroRNA (microRNA) is an endogenous non-coding small RNA with a length of 18-25 nucleotide single strands. It mainly inhibits its translation by completely or incompletely pairing with the 3' untranslated region of the target gene, thereby participating in the regulation of life activities such as individual development, cell apoptosis, proliferation and differentiation. Under pathological conditions, microRNAs can affect the occurrence and development of tumors by regulating their target genes and the signaling pathways they participate in, and play a role similar to oncogenes or tumor suppressor genes. Experiments have shown that in many tumors, some types of microRNAs are highly expressed, and these highly expre...

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Application Information

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IPC IPC(8): G06F19/14C12Q1/68G16B10/00
Inventor 曾华宗
Owner SHANGHAI CLUSTER BIOTECH