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CutFree

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Identifies the most diverse randomer that is free of recognition sites for any set of restriction enzymes. CutFree converts the problem of blocking restriction sites into a mixed-integer linear program (MILP) that returns a site-free randomer of maximum diversity. It can be applied to block a randomer of any length from containing arbitrary sequences. This tool ensures large numbers of barcode sequences and is compatible with restriction enzyme assembly methods like Golden Gate cloning.

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CutFree forum

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CutFree classification

CutFree specifications

Interface:
Web user interface
Programming languages:
R
Stability:
Stable
Maintained:
Yes
Restrictions to use:
Academic or non-commercial use
Computer skills:
Basic
Source code URL:
https://github.com/jensenlab/cutfree

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CutFree versioning

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CutFree classification

CutFree specifications

Software type:
Application/Script
Restrictions to use:
Academic or non-commercial use
Programming languages:
R
Stability:
Stable
Source code URL:
https://github.com/jensenlab/cutfree
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Maintained:
Yes

CutFree support

Maintainer

  • Paul Jensen <>
  • Paul Jensen <>

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Publications

Institution(s)

Department of Bioengineering and Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA

Funding source(s)

Supported by the NIH National Institute of Dental and Craniofacial Research (grant DE026817) and the University of Illinois at Urbana-Champaign.

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