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Bioinformatics Advance Access published online on April 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti460
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 8, 2004
Revised April 15, 2005
Accepted April 20, 2005

Applications note

{delta}{rho}-web, an online tool to assess composition similarity of individual nucleic acid sequences

M. W. J. van Passel 1, A. C. M. Luyf 2, A. H. C. van Kampen 2, A. Bart 1, and A. van der Ende 1*

1 Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
2 Bioinformatics Laboratory, Academic Medical Center, Amsterdam, the Netherlands

* To whom correspondence should be addressed.
A. van der Ende, E-mail: a.vanderende{at}amc.uva.nl


  Abstract

Summary: Although whole genome sequences have been analysed for the presence of anomalous DNA, no dedicated application is currently available to analyse the composition of individual sequence entries, for instance those derived by experimental techniques such as subtractive hybridisation. Since genomic dinucleotide frequency values are conserved between related species, a representative genome sequence can often be found to score for anomalous sequence composition for many of these putative horizontally transferred sequences. We developed the application {delta}{rho}-web, which enables the determination of the differences between the dinucleotide composition of an input sequence and that of a selected genome in a size dependent way. A feature allowing batch comparisons is included as well. In addition, {delta}{rho}-web allows the analysis of the dinucleotide composition of complete genomes. This provides complementary information for the identification of large anomalous gene clusters.

Availability: The application is available through http://deltarho.amc.uva.nl and the software is available from the authors.

Supplementary information: An online help file with more extensive user guidelines is supplied at http://deltarho.amc.uva.nl.


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