Gene orthology assessment with orthologID

Mary Egan, Ernest K. Lee, Joanna C. Chiu, Gloria Coruzzi, Rob Desalle

Research output: Chapter in Book/Report/Conference proceedingChapter


OrthologID ( allows for the rapid and accurate identification of gene orthology within a character-based phylogenetic framework. The Web application has two functions - an orthologous group search and a query orthology classification. The former determines orthologous gene sets for complete genomes and identifies diagnostic characters that define each orthologous gene set; and the latter allows for the classification of unknown query sequences to orthology groups. The first module of the Web application, the gene family generator, uses an E-value based approach to sort genes into gene families. An alignment constructor then aligns members of gene families and the resulting gene family alignments are submitted to the tree builder to obtain gene family guide trees. Finally, the diagnostics generator extracts diagnostic characters from guide trees and these diagnostics are used to determine gene orthology for query sequences.

Original languageEnglish (US)
Title of host publicationBioinformatics for DNA Sequence Analysis
EditorsDavid Posada
Number of pages16
StatePublished - 2009

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Single linkage cluster
  • alignment
  • diagnosis genomics
  • orthology
  • phylogeny

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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