Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences

Bioinformatics. 2005 Jul 1;21(13):3053-5. doi: 10.1093/bioinformatics/bti460. Epub 2005 Apr 26.

Abstract

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 deltarho-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, deltarho-web allows the analysis of the dinucleotide composition of complete genomes. This provides complementary information for the identification of large anomalous gene clusters.

MeSH terms

  • Algorithms*
  • Chromosome Mapping / methods*
  • Conserved Sequence
  • Internet*
  • Online Systems
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Sequence Homology, Nucleic Acid
  • Software*
  • User-Computer Interface*