Flicker of CRP vs FNR

Two sequence logos alternating about once a second. One is for 16 FNA binding sites and the other is for 58 CRP binding sites. That the logos are similar can be seen by the rapid comparison.

CRP and FNR are DNA binding proteins in E. coli. They have similar structures and they are both activators of transcription (for different sets of genes). Normally they do not bind to each other's sites, but mutation of the proteins has switched their binding sites, and changes to the DNA can allow the other protein to bind. It is therefore not surprising that the sequence logos of the sites are similar. By comparing the two sequence logos, we can gain some insight into the evolutionary divergence of the protein recognition process.

The display was inspired by Pete Lemkin's Flicker program. Mol Biotechnol. 1999 Sep;12(2):159-72. Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database. Lemkin PF, Thornwall G.

This image was created by combining two gif images using gifmerge. The gifs were created with xv from the PostScript. HOWEVER, I now strongly recommend that you use ImageMagick (http://www.imagemagick.org) instead. It is much more powerful.

Web accessiblity

Section 508 flicker requirements
To avoid photosensitive epilepsy Section 508 requires "(j) Pages shall be designed to avoid causing the screen to flicker with a frequency greater than 2 Hz and lower than 55 Hz." The gifmerge program allows one to set the delay time in 100ths of a second. So a delay of "-50" is 100/50 or 2 Hz. This is just at the limit. To be outside the range, I used a delay of "-60" or 100/60 = 1.7 Hz.

Logo Comparison methods:

  1. Plot Ri of of one model against the other model for all sequences. Use the unix paste to combine two scans and xyplo to plot.
  2. Use diffribl
  3. Flicker: https://alum.mit.edu/www/toms/flicker.html, this page.

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Schneider Lab
origin: 1997 February 6
updated: 2018 Mar 14
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