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Bioinformatics Advance Access originally published online on April 26, 2005
Bioinformatics 2005 21(13):3053-3055; 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{at}oupjournals.org

{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,*

1Department of Medical Microbiology, Academic Medical Center 1100 DE Amsterdam, The Netherlands
2Bioinformatics Laboratory, Academic Medical Center 1100 DE Amsterdam, The Netherlands

*To whom correspondence should be addressed.

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 hybridization. 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 manner. 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.

Contact: a.vanderende{at}amc.uva.nl

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


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