CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-01

AUTHORS

Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, Hisanori Kiryu

ABSTRACT

RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP-RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts. CapR is available at https://sites.google.com/site/fukunagatsu/software/capr. More... »

PAGES

r16

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/gb-2014-15-1-r16

DOI

http://dx.doi.org/10.1186/gb-2014-15-1-r16

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1007512395

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24447569


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/gb-2014-15-1-r16'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/gb-2014-15-1-r16'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gb-2014-15-1-r16'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gb-2014-15-1-r16'


 

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