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ViRBase: a resource for virus-host ncRNA-associated interactions.

Li Y, Wang C, Miao Z, Bi X, Wu D, Jin N, Wang L, Wu H, Qian K, Li C, Zhang T, Zhang C, Yi Y, Lai H, Hu Y, Cheng L, Leung KS, Li X, Zhang F, Li K, Li X, Wang D - Nucleic Acids Res. (2014)

Bottom Line: Viruses can use diverse ncRNAs to manipulate both cellular and viral gene expression to establish a host environment conducive to the completion of the viral life cycle.Many host cellular ncRNAs can also directly or indirectly influence viral replication and even target virus genomes.Users can query, browse and manipulate these virus-host ncRNA-associated interactions.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Peking University Health Science Center, Beijing, China.

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Related in: MedlinePlus

Representative screenshots of the Binding pages. The Binding page represents the predicted binding sites and scores between ncRNAs and their corresponding interactor by various of the predictor tools.
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Figure 3: Representative screenshots of the Binding pages. The Binding page represents the predicted binding sites and scores between ncRNAs and their corresponding interactor by various of the predictor tools.

Mentions: The identification of RNA-associated binding sites can provide valuable insights into the underlying regulatory mechanisms of various ncRNAs, thus the ‘Binding’ page of ViRBase also incorporates several useful tools to analyze the predicted binding site information for these interactions (Figure 3). For ncRNA–RNA interactions, the binding sites and scores are predicted according to miRanda (16) and RIsearch (17). For ncRNA–protein interactions, RNA-binding residues and scores are computed by bindN+ (18) and RNAbindR (19), while the experimentally verified RNA-binding sites documented in RBPBD (20) are also integrated. The parameters used by these tools were documented in the ‘Parameter’ field of the ‘Help’ page.


ViRBase: a resource for virus-host ncRNA-associated interactions.

Li Y, Wang C, Miao Z, Bi X, Wu D, Jin N, Wang L, Wu H, Qian K, Li C, Zhang T, Zhang C, Yi Y, Lai H, Hu Y, Cheng L, Leung KS, Li X, Zhang F, Li K, Li X, Wang D - Nucleic Acids Res. (2014)

Representative screenshots of the Binding pages. The Binding page represents the predicted binding sites and scores between ncRNAs and their corresponding interactor by various of the predictor tools.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384010&req=5

Figure 3: Representative screenshots of the Binding pages. The Binding page represents the predicted binding sites and scores between ncRNAs and their corresponding interactor by various of the predictor tools.
Mentions: The identification of RNA-associated binding sites can provide valuable insights into the underlying regulatory mechanisms of various ncRNAs, thus the ‘Binding’ page of ViRBase also incorporates several useful tools to analyze the predicted binding site information for these interactions (Figure 3). For ncRNA–RNA interactions, the binding sites and scores are predicted according to miRanda (16) and RIsearch (17). For ncRNA–protein interactions, RNA-binding residues and scores are computed by bindN+ (18) and RNAbindR (19), while the experimentally verified RNA-binding sites documented in RBPBD (20) are also integrated. The parameters used by these tools were documented in the ‘Parameter’ field of the ‘Help’ page.

Bottom Line: Viruses can use diverse ncRNAs to manipulate both cellular and viral gene expression to establish a host environment conducive to the completion of the viral life cycle.Many host cellular ncRNAs can also directly or indirectly influence viral replication and even target virus genomes.Users can query, browse and manipulate these virus-host ncRNA-associated interactions.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Peking University Health Science Center, Beijing, China.

Show MeSH
Related in: MedlinePlus