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Related Concept Videos

MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
Pre-mRNA Processing02:01

Pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...
pre-mRNA Processing02:01

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...
Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps the cell...

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Updated: Jun 28, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation
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mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

Identification of microRNA precursors with support vector machine and string kernel.

Jian-Hua Xu1, Fei Li, Qiu-Feng Sun

  • 1Department of Computer Science, Nanjing Normal University, Nanjing 210097, China. xujianhua@njnu.edu.cn

Genomics, Proteomics & Bioinformatics
|November 1, 2008
PubMed
Summary

This study introduces a novel method using sequence and structure data to accurately identify true microRNA precursors (pre-miRNAs). The approach significantly improves detection rates, especially for complex pre-miRNAs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • MicroRNAs (miRNAs) are crucial regulatory non-coding RNAs.
  • Accurate identification of miRNA precursors (pre-miRNAs) is vital for miRNA research.
  • Existing methods using numerical features may miss discriminative information in pre-miRNA sequences and structures.

Purpose of the Study:

  • To develop a computational method for distinguishing true from false pre-miRNAs.
  • To leverage both sequence and secondary structure information directly.
  • To improve the accuracy of pre-miRNA identification, including complex structures.

Main Methods:

  • Constructed an exponential kernel based on weighted Levenshtein distance for pre-miRNA sequences and structures.
  • Integrated the string kernel with Support Vector Machine (SVM) for classification.
  • Optimized SVM parameters using 5-fold cross-validation and grid search on human pre-miRNA data.

Main Results:

  • The proposed method outperformed previous SVM-based techniques on 11 out of 16 independent test sets.
  • Achieved a high accuracy of 92.66% in identifying pre-miRNAs, including those with multiple loops.
  • Demonstrated superior performance across human, animal, plant, and viral pre-miRNA datasets.

Conclusions:

  • Directly utilizing pre-miRNA sequences and secondary structures with a novel string kernel enhances detection accuracy.
  • The method effectively identifies challenging pre-miRNA structures previously excluded.
  • This approach offers a robust tool for computational miRNA identification.