Measuring the functional sequence complexity of proteins.
BACKGROUND
Abel and Trevors have delineated three aspects of sequence complexity, Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC) observed in biosequences such as proteins. In this paper, we provide a method to measure functional sequence complexity.


RESULTS
We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families. Considerations were made in determining how the measure can be used to correlate functionality when relating to the whole molecule and sub-molecule. In the experiment, we show that when the proposed measure is applied to the aligned protein sequences of ubiquitin, 6 of the 7 highest value sites correlate with the binding domain.


CONCLUSIONS
For future extensions, measures of functional bioinformatics may provide a means to evaluate potential evolving pathways from effects such as mutations, as well as analyzing the internal structural and functional relationships within the 3-D structure of proteins.
Department of Biophysics, University of Guelph, Guelph, ON, N1G 2W1, Canada. kdurston@uoguelph.ca
Kirk K
KK
Durston
David K Y
DK
Chiu
David L
DL
Abel
Jack T
JT
Trevors
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D005810:Multigene Family; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000235:genetics / Q000502:physiology*; D020539:Sequence Analysis, Protein; D012984:Software; D035501:Uncertainty
D011506:Proteins