title: Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).
abstract: Comparative genomics promises to rapidly accelerate the identification and functional classification of biologically important human genes. We developed the TIGR Orthologous Gene Alignment (TOGA; <http://www.tigr.org/tdb/toga/toga.shtml>) database to provide a cross-reference between fully and partially sequenced eukaryotic transcribed sequences. Starting with the assembled expressed sequence tag (EST) and gene sequences that comprise the 28 TIGR Gene Indices, we used high-stringency pair-wise sequence searches and a reflexive, transitive closure process to associate sequence-specific best hits, generating 32,652 tentative ortholog groups (TOGs). This has allowed us to identify putative orthologs and paralogs for known genes, as well as those that exist only as uncharacterized ESTs and to provide links to additional information including genome sequence and mapping data. TOGA provides an important new resource for the analysis of gene function in eukaryotes. In addition, an analysis of the most widely represented sequences can begin to provide insight into eukaryotic biological processes.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland 20850, USA.
authors.forename: Yuandan
authors.initials: Y
authors.lastname: Lee
authors.forename: Razvan
authors.initials: R
authors.lastname: Sultana
authors.forename: Geo
authors.initials: G
authors.lastname: Pertea
authors.forename: Jennifer
authors.initials: J
authors.lastname: Cho
authors.forename: Svetlana
authors.initials: S
authors.lastname: Karamycheva
authors.forename: Jennifer
authors.initials: J
authors.lastname: Tsai
authors.forename: Babak
authors.initials: B
authors.lastname: Parvizi
authors.forename: Foo
authors.initials: F
authors.lastname: Cheung
authors.forename: Valentin
authors.initials: V
authors.lastname: Antonescu
authors.forename: Joseph
authors.initials: J
authors.lastname: White
authors.forename: Ingeborg
authors.initials: I
authors.lastname: Holt
authors.forename: Feng
authors.initials: F
authors.lastname: Liang
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
mesh_terms: D000465:Algorithms; D000818:Animals; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D016384:Consensus Sequence / Q000235:genetics; D030541:Databases, Genetic; D005057:Eukaryotic Cells / Q000737:chemistry / Q000378:metabolism; D005796:Genes / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D051379:Mice; D010802:Phylogeny; D051381:Rats; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid