Peakhood: individual site context extraction for CLIP-seq peak regions
Abstract: Motivation
CLIP-seq is by far the most widely used method to determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). The binding site locations are identified from CLIP-seq read data by tools termed peak callers. Many RBPs bind to a spliced RNA (i.e. transcript) context, but all currently available peak callers only consider and report the genomic context. To accurately model protein binding behavior, a tool is needed for the individual context assignment to CLIP-seq peak regions.
Results
Here we present Peakhood, the first tool that utilizes CLIP-seq peak regions identified by peak callers, in tandem with CLIP-seq read information and genomic annotations, to determine which context applies, individually for each peak region. For sites assigned to transcript context, it further determines the most likely splice variant, and merges results for any number of datasets to obtain a comprehensive collection of transcript context binding sites
- Location
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Deutsche Nationalbibliothek Frankfurt am Main
- Extent
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Online-Ressource
- Language
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Englisch
- Notes
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Bioinformatics. - 38, 4 (2022) , 1139-1140, ISSN: 1460-2059
- Event
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Veröffentlichung
- (where)
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Freiburg
- (who)
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Universität
- (when)
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2022
- Creator
- DOI
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10.1093/bioinformatics/btab755
- URN
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urn:nbn:de:bsz:25-freidok-2319985
- Rights
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Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
- Last update
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25.03.2025, 1:43 PM CET
Data provider
Deutsche Nationalbibliothek. If you have any questions about the object, please contact the data provider.
Associated
- Uhl, Michael
- Rabsch, Dominik
- Eggenhofer, Florian
- Backofen, Rolf
- Universität
Time of origin
- 2022
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A complete axiomatization of a theory with feature and arity constraints
Improving CLIP-seq data analysis by incorporating transcript information
Standardization of CLIP-seq data analysis and optimization of related peak calling to investigate RNA-protein interactions
Expressivity and decidability of first-order languages over feature trees
Expressivity and decidability of first-order languages over feature trees
StoatyDive: evaluation and classification of peak profiles for sequencing data
A complete axiomatization of a theory with feature and arity constraints
Regular path expressions in feature logic
RIP-Seq suggests translational regulation by L7Ae in Archaea
Optimizing algorithms for the comparative analysis of non-coding RNAs
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Computational analyses of post-transcriptional regulatory mechanisms : = Computergestützte Analysen von post-transkriptionellen regulatorischen Mechanismen