Bioinformatics for DNA Sequence Analysis

Volume 537 of the series Methods in Molecular Biology pp 23-38


Gene Orthology Assessment with OrthologID

  • Mary EganAffiliated withDepartment of Biology, Montclair State University
  • , Ernest K. LeeAffiliated withDepartment of Biology, New York University
  • , Joanna C. ChiuAffiliated withDepartment of Molecular Biology and Biochemistry, Rutgers University
  • , Gloria CoruzziAffiliated withDepartment of Biology, New York University
  • , Rob DeSalleAffiliated withSackler Institute of Comparative Genomics, American Museum of Natural History New York

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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