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cWords

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Regulates motif discovery in differential case–control mRNA expression datasets. cWords can identify potential siRNA off-target binding. It is based on rigorous statistical methods that demonstrate comparable or better performance than other existing methods. The tool is based on a binomial model with a kth-order Markov Model that corrects for composition bias in each sequence. It can rank words across different word lengths and uses clustering to group similar words.

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cWords classification

cWords specifications

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

cWords distribution

download

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cWords classification

cWords specifications

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

cWords distribution

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cWords support

Documentation

Maintainer

  • Anders Krogh <>
  • Anders Krogh <>

Credits

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Publications

Institution(s)

Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

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.

Link to literature

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