An automated phylogenetic key for classifying homeoboxes.
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.
Sarkar
I Neil
IN
Department of Medical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA.
Thornton
Joseph W
JW
Planet
Paul J
PJ
Figurski
David H
DH
Schierwater
Bernd
B
DeSalle
Rob
R
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
D018398:Homeodomain Proteins