%0 Journal Article
%T Measuring the functional sequence complexity of proteins
%A Kirk K Durston
%A David KY Chiu
%A David L Abel
%A Jack T Trevors
%J Theoretical Biology and Medical Modelling
%D 2007
%I BioMed Central
%R 10.1186/1742-4682-4-47
%X 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.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.There has been increasing recognition that genes deal with information processing. They have been referred to as "subroutines within a much larger operating system". For this reason, approaches previously reserved for computer science are now increasingly being applied to computational biology [1]. If genes can be thought of as information-processing subroutines, then proteins can be analyzed in terms of the products of information interacting with laws of physics. It may be possible to advance our knowledge of proteins, such as their structure and functions, by examining the patterns of functional information when studying a protein family.Our proposed method is based on mathematical and computational concepts (e.g., measures). We show here that, at least in some cases in sequence analysis, the proposed measure is useful in analyzing protein families with interpretable experimental results.Abel and Trevors have delineated three qualitative aspects of linear digital sequence co
%U http://www.tbiomed.com/content/4/1/47