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cWords specifications

Information


Unique identifier OMICS_16680
Name cWords
Interface Web user interface
Restrictions to use None
Input data A RNA or DNA sequence.
Programming languages Ruby
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Download


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Documentation


Maintainer


  • person_outline Anders Krogh

Information


Unique identifier OMICS_16680
Name cWords
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A RNA or DNA sequence.
Operating system Unix/Linux, Mac OS
Programming languages Ruby
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Download


download.png
github.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Anders Krogh

Publication for cWords

cWords citations

 (3)
library_books

TGF β induces miR 100 and miR 125b but blocks let 7a through LIN28B controlling PDAC progression

2018
Nat Commun
PMCID: 5945639
PMID: 29748571
DOI: 10.1038/s41467-018-03962-x

[…] a novel approach to integrate miRNA overexpression with AGO2 RNA immunoprecipitation (RIP) sequencing (RIP-seq) and differential expression analysis within a bioinformatics framework with Sylamer and cWords algorithms–. We called this method RIP followed by Unbiased Sequence Enrichment analysis (RIP-USE) (Fig.  and Methods). This method is developed in several steps (Fig. ), including overexpressi […]

library_books

Highly accessible AU rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

2017
PLoS Comput Biol
PMCID: 5409497
PMID: 28410363
DOI: 10.1371/journal.pcbi.1005460

[…] bability that at least 20 consecutive nucleotides are unpaired (). This result is consistent with the fact that hotspots are more accessible regions, which favors the binding of multiple RBPs.We used cWords [] to identify motifs enriched in hotspots. We identified several AREs, including UAUUUAU, among the top 20 ranked words enriched both in hotspots and in conserved regions (). The core ARE elem […]

library_books

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F actin formation

2015
Genome Biol
PMCID: 4477473
PMID: 26054396
DOI: 10.1186/s13059-015-0687-0

[…] ls (average of less than five reads per nucleotide), and selected the 25,000 most enriched clusters in 3′ UTRs. These sequences and the enrichment ranking were subjected to the motif discovery method cWords [] in two separate analyses, one for each iCLIP protocol. […]

Citations

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cWords institution(s)
Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
cWords funding source(s)
Supported by grants from the Danish Strategic Research Council and from the Novo Nordisk Foundation and by a grant from the Danish Research Council.

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