Exp. Biol. Med. 2008;233:665-673
doi:10.3181/0704-MR-97
© 2008 Society for Experimental Biology and Medicine
Harlan Robins*1,
Michael Krasnitz and
Arnold J. Levine
* Computational Biology Group, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109; and Institute for Advanced Study, Princeton, New Jersey 08540
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Figure 1. Outline of Robins-Krasnitz algorithm. Figure 1 shows a flow chart of the steps in the Robins-Krasnitz algorithm. The process is iterated with a new motif added to the output at each step. |
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Figure 2. Example of shuffling procedure. The procedure to get the maximal entropy distribution (MED) involves a set of randomized iterations. The triplets of nucleotides coding for each amino acid are permuted randomly among themselves. This is an illustrative example of mock short protein with eight amino acids. The shuffling procedure randomly permutes L1, L2, L3, and L4 and separately permutes H1, H2, and H3. Each iteration produces a new sequence. For this example, there are 12 different combinations for the Leucines and three combinations for the Histidines giving 36 unique sequences. They are weighted in the shuffling procedure so that the MED is attained in the limit of a large number of iterations. |
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Figure 3. A bacterial phylogenetic tree using a metric based solely on motifs differences. Figure 3A is the phylogenetic tree for the 164 bacterial species found in the NCBI database. The black rectangle encloses the Enterobacteria clade. Figure 3B contains a blow up of this section of the tree. The only Enterobacteria missing from this group is Buchnera Aphidicola. |
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