Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments

Bioinformatics. 2006 Jun 15;22(12):1536-7. doi: 10.1093/bioinformatics/btl151. Epub 2006 Apr 21.


Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. In a typical scenario, two groups of aligned sequences will share a common motif but will differ in their functional annotation. The inclusion of the background alignment provides an appropriate underlying amino acid or nucleotide distribution and addresses intersite symbol correlations. In addition, the difference detection process is sensitive to the sizes of the aligned groups. Two Sample Logo extends WebLogo, a widely-used sequence logo generator. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge.

MeSH terms

  • Algorithms
  • Alternative Splicing
  • Base Sequence
  • Computational Biology / methods*
  • Computer Graphics*
  • Exons
  • Humans
  • Internet
  • Introns
  • Models, Statistical
  • Molecular Sequence Data
  • Programming Languages
  • Sequence Alignment / methods*
  • Thermodynamics