• Sequence Logos and the Helix of DNA (PDF)

Topics:

I give talks about molecular information theory, including information theory, sequence logos, sequence walkers, and the theory of molecular machines. My standard talk

One hour talks generally have two parts:

• Introduction to Molecular Information Theory. The first half hour covers essential introductory material: information theory, sequence logos and sequence walkers (i.e. Level 0 theory).

• The second half hour delves into one of three alternatives:

  1. Evolution of Binding Sites. Introduces the concept of Rsequence ~ Rfrequency, which was my PhD thesis in 1984 and then shows how Rsequence evolves towards Rfrequency. The slides are online. This material is essential to understanding molecular information theory but I frequently do not cover the topic since it is so old. It was published in the Ev paper.

  2. Flippers, Flappers and Flip-Flops in DNA Binding. This corresponds to three papers published in Nucleic Acids Research (baseflip, repan3 and fff) and a patent on molecular computing. Besides these materials, a general abstract is available. This material demonstrates clearly what is missed if one uses consensus sequences.

  3. Theory of Molecular Machines (Levels 1 - 4). An introduction to molecular machine efficiency, as described in the Press release for the 1998 AAAS Annual meeting. The abstract is available online. This is the most advanced, recent, and therefore (for me at least!) fascinating, material. It is now published in the emmgeo paper.

These talks are designed to be 1 or 2 hours long (including questions). Because the four segments take about a half hour each, all of these topics can be covered in two hours, in the order given above. In one hour I give the introduction followed by one of the three second halves. If I have less than an hour I will have to skip parts of the second topic, because the first part of the talk is required to get people up to steam.

Bibliography for Tom Schneider

Picture of Tom Schneider

Thank you for your invitation!

  Thomas D. Schneider, Ph.D.
  toms@alum.mit.edu
  https://alum.mit.edu/www/toms