title: OrthologID: automation of genome-scale ortholog identification within a parsimony framework.
abstract: BACKGROUND
  The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation.
  
  
  RESULTS
  We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.
  
  
  BACKGROUND
  http://nypg.bio.nyu.edu/orthologid/
authors.affiliation: Department of Biology, New York University, New York, NY 10003, USA.
authors.forename: Joanna C
authors.initials: JC
authors.lastname: Chiu
authors.forename: Ernest K
authors.initials: EK
authors.lastname: Lee
authors.forename: Mary G
authors.initials: MG
authors.lastname: Egan
authors.forename: Indra Neil
authors.initials: IN
authors.lastname: Sarkar
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Coruzzi
authors.forename: Rob
authors.initials: R
authors.lastname: DeSalle
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics; D030541:Databases, Genetic; D010363:Pattern Recognition, Automated / Q000379:methods; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface