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A method for predicting microRNAs in non-model organisms

A biological and model technology, applied in special data processing applications, instruments, electronic digital data processing, etc., can solve problems such as difficulty in obtaining whole genome sequence data and difficulty in microRNA prediction

Inactive Publication Date: 2011-12-07
SHANGHAI CLUSTER BIOTECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For model organisms with simple structures and small genomes, it is still difficult for most non-model organisms to obtain their whole genome sequence data, which makes the prediction of microRNA in non-model organisms difficult

Method used

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  • A method for predicting microRNAs in non-model organisms
  • A method for predicting microRNAs in non-model organisms
  • A method for predicting microRNAs in non-model organisms

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Experimental program
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Embodiment Construction

[0015] The method of the present invention will take the microRNA prediction of the non-model organism planarian (Schmidtea mediterannea) as an example, and describe the steps of the specific implementation of the method:

[0016] 1. Download the gene sequence data of the target species from the online gene database. The present invention downloads the known gene sequence data of Schmidtea mediterannea from Gene Center

[0017] (http: / / genome.wustl.edu / pub / organism / Invertebrates / Schmidtea_mediterrannea / assembly / Schmidtea_mediterranea-3.1 / output / supercontigs.fa.gz)

[0018] 2. Use the online de-duplication tool repeatmasker

[0019] (http: / / www.repeatmasker.org / cgi-bin / WEBRepeatMasker), import the gene sequence of Schmidteamediterannea, select the default parameters to execute, and remove the repetitive sequence in the genome.

[0020] 3. Use Srnaloop software to scan the above de-repeated sequence, extract the sequence of the clasp structure, and set the parameters as: -w 5-...

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Abstract

The present invention designs a method for predicting microRNA in non-model organisms. The method includes the following steps: step 1, downloading the corresponding non-model organism genome sequence from the Internet; step 2, removing repetitive sequences in the genome; extract the hairpin ring structure; Step 4, screen and remove hairpin rings with inappropriate GC content and unstable secondary structure; Step 5, predict the hairpin rings, and extract hairpin rings with similar characteristics to the precursor microRNA; Step 6, remove Loop sequences that are poorly conserved among species are compared with mature microRNAs of all known species to obtain possible microRNAs; step 7, perform statistical analysis on the prediction results.

Description

technical field [0001] The patent of this invention belongs to the field of biotechnology and relates to a method for predicting microRNA in non-model organisms Background technique [0002] MicroRNA (micro ribonucleic acid) is an endogenous non-coding small RNA with a length of 19-25 nucleotides. It mainly inhibits its translation through complete or incomplete 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 expressed microRNAs are related to tumor invasion and metastasis. [0003] ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68G06F19/24
Inventor 曾华宗
Owner SHANGHAI CLUSTER BIOTECH