Efficient Boolean implementation of universal sequence maps (bUSM).
BACKGROUND
Recently, Almeida and Vinga offered a new approach for the representation of arbitrary discrete sequences, referred to as Universal Sequence Maps (USM), and discussed its applicability to genomic sequence analysis. Their work generalizes and extends Chaos Game Representation (CGR) of DNA for arbitrary discrete sequences.


RESULTS
We have considered issues associated with the practical implementation of USMs and offer a variation on the algorithm that: 1) eliminates the overestimation of similar segment lengths, 2) permits the identification of arbitrarily long similar segments in the context of finite word length coordinate representations, 3) uses more computationally efficient operations, and 4) provides a simple conversion for recovering the USM coordinates. Computational performance comparisons and examples are provided.


CONCLUSIONS
We have shown that the desirable properties of the USM encoding of nucleotide sequences can be retained in a practical implementation of the algorithm. In addition, the proposed implementation enables determination of local sequence identity at increased speed.
Schwacke
John
J
Department of Biometry and Epidemiology, Medical University of South Carolina, 135 Cannon Street, Suite 303, PO Box 250835, Charleston, SC 29425, USA. schwacke@musc.edu
Almeida
Jonas S
JS
D000465:Algorithms; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D008128:Logic; D017711:Nonlinear Dynamics; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data*