title: An automated phylogenetic key for classifying homeoboxes.
abstract: When novel gene sequences are discovered, they are usually identified, classified, and annotated based on aggregate measures of sequence similarity. This method is prone to errors, however. Phylogenetic analysis is a more accurate basis for gene classification and ortholog identification, but it is relatively labor-intensive and computationally demanding. Here we report and demonstrate a rapid new method for gene classification based on phylogenetic principles. Given the phylogeny of a minimal sample of gene family members, our method automatically identifies amino acids that are phylogenetically characteristic of each class of sequences in the family; it then classifies a novel sequence based on the presence of these characteristic attributes in its sequence. Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time.
authors.affiliation: Department of Medical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA.
authors.forename: I Neil
authors.initials: IN
authors.lastname: Sarkar
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Thornton
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Planet
authors.forename: David H
authors.initials: DH
authors.lastname: Figurski
authors.forename: Bernd
authors.initials: B
authors.lastname: Schierwater
authors.forename: Rob
authors.initials: R
authors.lastname: DeSalle
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001331:Automation; D019992:Databases as Topic; D004330:Drosophila; D018398:Homeodomain Proteins / Q000145:classification* / Q000235:genetics*; D006801:Humans; D020407:Internet; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D014231:Tribolium / Q000235:genetics; D015027:Zebrafish
chemical_list: D018398:Homeodomain Proteins