Bioinformatics Vol. 18 no. 4 2002
Pages 507-512
© 2002 Oxford University Press
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise
Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
Received on August 28, 2001
; revised on October 31, 2001
; accepted on November 2, 2001
Motivation: Calculation of the information content of motifsin genomes highly biased in nucleotide composition is likely to lead to overestimates of the amount of useful informationin the motif. Calculating relative information can compensate for biases, however the resulting information content is the amount seen by an observer and not by a macromolecule binding to the motif. The latter is needed to calculate the discriminatory power of the motif and to compare motifs between species.
Results: By treating a biased genome as a discrete channel with noise, in accordance with Shannon Information Theory, we were able to remove both ‘Distortion’ and ‘Noise’ from the motif and recover a more instructive biological ‘signal.’ A Java application, LogoPaint, was developed to remove nucleotide bias distortion and triplet frequency noise from motifs, calculate information content and present the motif as a logo. We demonstrate how this technique can ‘unmask’ motifs in the translation initiation regions of bacteria that are obscured by strong sequence biases.
Availability: LogoPaint is available to all users from the authors as an executable JAR file. Source code is available by arrangement.
Contact: chris.brown{at}stonebow.otago.ac.nz
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  V. Jensen, D. Lons, C. Zaoui, F. Bredenbruch, A. Meissner, G. Dieterich, R. Munch, and S. Haussler RhlR Expression in Pseudomonas aeruginosa Is Modulated by the Pseudomonas Quinolone Signal via PhoB-Dependent and -Independent Pathways J. Bacteriol., December 15, 2006; 188(24): 8601 - 8606. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Hasan and M. Schreiber Recovering motifs from biased genomes: application of signal correction Nucleic Acids Res., October 6, 2006; (2006) gkl676v3. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Reents, R. Munch, T. Dammeyer, D. Jahn, and E. Hartig The Fnr Regulon of Bacillus subtilis J. Bacteriol., February 1, 2006; 188(3): 1103 - 1112. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Hiller, A. Grote, M. Scheer, R. Munch, and D. Jahn PrediSi: prediction of signal peptides and their cleavage positions Nucleic Acids Res., July 1, 2004; 32(suppl_2): W375 - W379. [Abstract] [Full Text] [PDF]
|
|