More powerful discriminants for classifying phylogenetic signals in dinucleotide frequencies

Robert H. Baran, Changwon Jeon, David K. Han, Hanseok Ko

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Microbial DNA fragments are classified according to species using compositional features and "genomic signatures" the oldest of which is the dinucleotide relative abundance profile defined by Karlin et al. More informative features, including higher order signatures, have demonstrated greater species-specificity in comparison to the baseline established by the dinucleotide signature using "delta-distance" to assess dissimilarity; but lack of standard methods has precluded rigorous comparison. We describe a new method for classifier evaluation that reduces any number of pair-wise inter-genomic comparisons to a single performance measure. To illustrate the method, we compare delta-distance to quadratic and linear discriminants prescribed by elementary pattern recognition theory, and find that the quadratic form is significantly more powerful.

Original languageEnglish
Title of host publication2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
Pages605-608
Number of pages4
DOIs
Publication statusPublished - 2008
Event2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP - Las Vegas, NV, United States
Duration: 2008 Mar 312008 Apr 4

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
ISSN (Print)1520-6149

Other

Other2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
CountryUnited States
CityLas Vegas, NV
Period08/3/3108/4/4

Keywords

  • Biomedical signal processing
  • DNA
  • Error analysis
  • Pattern classification
  • Software performance

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

Fingerprint Dive into the research topics of 'More powerful discriminants for classifying phylogenetic signals in dinucleotide frequencies'. Together they form a unique fingerprint.

Cite this