Gavin E. Crooks

Gavin E. Crooks

Bespoke research on non-equilibrium thermodynamics, quantum computing, and the physics of information.

Berkeley Institute for the Theoretical Sciences

Normal Computing

WebLogo 3.3 Released

3.3 (2012-07-02) [Gavin Crooks, David Sivak]

  • Improved the algorithm that guesses the sequence type (DNA, RNA or protein) (Kudos: Bug report, Roland Pache )
  • Fixed an issue with reading transfac matrices with alternative alphabets(Kudos: Bug report, Nima Emami )
  • Fixed Motif.reindex()
  • Implemented Motif.reverse() and Motif.complement() (Can now reverse complement transfac matrix input on the command line.) (Kudos: Feature request, Seth P Boudreaux )
  • Command line interface now automagically recognizes transfac files.
  • Add command line option “–reverse-stacks NO” which inverts the logo stacks so that the most conserved monomers are at the bottom of the stack, rather than the top. This ordering is consistent with the standard ordering for histograms, and is arguably a better representation. (Kudos: Luke Hutchison )
  • Fixed an issue so that the correct color scheme is chosen for the specified sequence type.

  • Miscellaneous minor bug fixes and refactoring.

  • WebLogo 3.3 web-sever
  • WebLogo 3.3 code

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We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.