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KAPAC
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KAPAC

KAPAC (for k-mer activity on polyadenylation site choice) is a tool to detect sequence motifs that affect poly(A) site usage on the 3' end. The package also includes PAQR (polyadenylation site usage quantification from RNA sequencing data) tool for evaluation of the 3' end processing in distinct data sets.



KAPAC

KAPAC (for k-mer activity on polyadenylation site choice) is a tool to detect sequence motifs that affect poly(A) site usage on the 3' end. The package also includes PAQR (polyadenylation site usage quantification from RNA sequencing data) tool for evaluation of the 3' end processing in distinct data sets.

Topic

Oncology; Pathology; RNA-seq

Details

  • Operation: Sequence analysis; Nucleic acid feature detection; PolyA signal detection
  • Software interface: Command-line user interface
  • Language: R;Python
  • Operating system: Linux; Mac OS X
  • License: GNU GPL v2
    • Cost: Free
  • Version name: -
  • Credit: Swiss National Science Foundation, National Center for Competence in Research "RNA & Disease."
  • Contact: Mihaela Zavolan mihaela.zavolan _at_ unibas.ch | Andreas J. Gruber aj.gruber _at_ unibas.ch | Ralf Schmidt ralf.schmidt _at_ unibas.ch | Souvik Ghosh souvik.ghosh _at_ unibas.ch | Georges Martin georges.martin _at_ unibas.ch | Andreas R. Gruber andreas _at_ paperpile.com | Erik van Nimwegen erik.vannimwegen _at_ unibas.ch
  • Collection: -

Publications

Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M "Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC." Genome Biol. 2018 Mar 28;19(1):44. https://doi.org/10.1186/s13059-018-1415-3
PMID: 29592812
PMCID: PMC5875010


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