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Related Concept Videos

Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Updated: Jun 7, 2025

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RASP v2.0: an updated atlas for RNA structure probing data.

Kunting Mu1,2,3, Yuhan Fei1,2,3, Yiran Xu1,2,3

  • 1MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Nucleic Acids Research
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Summary
This summary is machine-generated.

RASP v2.0 enhances RNA structure analysis with a larger dataset and new tools. This updated database aids in exploring RNA structure-function relationships across species.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA molecules are crucial for biological processes, performing functions through complex structures.
  • Understanding RNA structure is key to deciphering its biological roles.

Purpose of the Study:

  • To present RASP v2.0, an updated database for RNA structure probing data.
  • To enhance online structural analysis functionalities for RNA studies.

Main Methods:

  • Expanded the RNA structure dataset from 156 to 438 entries, including transcriptome-wide, target-specific, and RNA-RNA interaction datasets.
  • Implemented a deep learning model to impute missing structural signals in 59 datasets, improving data quality for low-abundance RNAs.
  • Deployed three new online analysis modules: missing structure score imputation, RNA secondary/tertiary structure prediction, and RNA binding protein (RBP) binding prediction.

Main Results:

  • RASP v2.0 now contains 438 RNA structure datasets, covering 24 species.
  • Deep learning imputation significantly improved data quality for low-coverage transcriptome-wide datasets.
  • New analysis modules offer advanced capabilities for RNA structure research.

Conclusions:

  • RASP v2.0 provides a more comprehensive resource for RNA structure data.
  • The enhanced functionalities facilitate the exploration of RNA structure-function relationships.
  • RASP v2.0 is a valuable tool for researchers studying diverse biological processes involving RNA.