Gene Orthology Assessment with OrthologID

  • Mary Egan
  • Ernest K. Lee
  • Joanna C. Chiu
  • Gloria Coruzzi
  • Rob DeSalle
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 537)

Abstract

OrthologID (http://nypg.bio.nyu.edu/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.

Key words

Single linkage cluster orthology phylogeny alignment diagnosis genomics 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Mary Egan
    • 1
  • Ernest K. Lee
    • 2
  • Joanna C. Chiu
    • 3
  • Gloria Coruzzi
    • 2
  • Rob DeSalle
    • 4
  1. 1.Department of BiologyMontclair State UniversityMontclairUSA
  2. 2.Department of BiologyNew York UniversityNew YorkUSA
  3. 3.Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayUSA
  4. 4.Sackler Institute of Comparative Genomics, American Museum of Natural History New YorkNew YorkUSA

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