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

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.

Original languageEnglish (US)
Title of host publicationBioinformatics for DNA Sequence Analysis
Pages23-38
Number of pages16
Volume537
DOIs
StatePublished - 2009

Publication series

NameMethods in Molecular Biology
Volume537
ISSN (Print)10643745

Fingerprint

Genes
Pedigree
Genome

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Egan, M., Lee, E. K., Chiu, J. C., Coruzzi, G., & Desalle, R. (2009). Gene orthology assessment with orthologID. In Bioinformatics for DNA Sequence Analysis (Vol. 537, pp. 23-38). (Methods in Molecular Biology; Vol. 537). https://doi.org/10.1007/978-1-59745-251-9_2

Gene orthology assessment with orthologID. / Egan, Mary; Lee, Ernest K.; Chiu, Joanna C.; Coruzzi, Gloria; Desalle, Rob.

Bioinformatics for DNA Sequence Analysis. Vol. 537 2009. p. 23-38 (Methods in Molecular Biology; Vol. 537).

Research output: Chapter in Book/Report/Conference proceedingChapter

Egan, M, Lee, EK, Chiu, JC, Coruzzi, G & Desalle, R 2009, Gene orthology assessment with orthologID. in Bioinformatics for DNA Sequence Analysis. vol. 537, Methods in Molecular Biology, vol. 537, pp. 23-38. https://doi.org/10.1007/978-1-59745-251-9_2
Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R. Gene orthology assessment with orthologID. In Bioinformatics for DNA Sequence Analysis. Vol. 537. 2009. p. 23-38. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-59745-251-9_2
Egan, Mary ; Lee, Ernest K. ; Chiu, Joanna C. ; Coruzzi, Gloria ; Desalle, Rob. / Gene orthology assessment with orthologID. Bioinformatics for DNA Sequence Analysis. Vol. 537 2009. pp. 23-38 (Methods in Molecular Biology).
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