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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
Published on: August 15, 2019
Gene orthology assessment with OrthologID
Mary Egan1, Ernest K Lee, Joanna C Chiu
1Department of Biology, Montclair State University, Montclair, NJ, USA.
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.
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