title: Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
abstract: Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology information is prerequisite for further studies. However, detection of orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, are utilized. Thus, as a sub-database of H-InvDB, an integrated database of annotated human genes (http://h-invitational.jp/), we constructed a fully curated database of evolutionary features of human genes, called 'Evola'. In the process of the ortholog detection, computational analysis based on conserved genome synteny and transcript sequence similarity was followed by manual curation by researchers examining phylogenetic trees. In total, 18 968 human genes have orthologs among 11 vertebrates (chimpanzee, mouse, cow, chicken, zebrafish, etc.), either computationally detected or manually curated orthologs. Evola provides amino acid sequence alignments and phylogenetic trees of orthologs and homologs. In 'd(N)/d(S) view', natural selection on genes can be analyzed between human and other species. In 'Locus maps', all transcript variants and their exon/intron structures can be compared among orthologous gene loci. We expect the Evola to serve as a comprehensive and reliable database to be utilized in comparative analyses for obtaining new knowledge about human genes. Evola is available at http://www.h-invitational.jp/evola/.
authors.affiliation: Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, Tokyo, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsuya
authors.forename: Ryuichi
authors.initials: R
authors.lastname: Sakate
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kawahara
authors.forename: Kanako O
authors.initials: KO
authors.lastname: Koyanagi
authors.forename: Yoshiharu
authors.initials: Y
authors.lastname: Sato
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Fujii
authors.forename: Chisato
authors.initials: C
authors.lastname: Yamasaki
authors.forename: Takuya
authors.initials: T
authors.lastname: Habara
authors.forename: Hajime
authors.initials: H
authors.lastname: Nakaoka
authors.forename: Fusano
authors.initials: F
authors.lastname: Todokoro
authors.forename: Kaori
authors.initials: K
authors.lastname: Yamaguchi
authors.forename: Toshinori
authors.initials: T
authors.lastname: Endo
authors.forename: Satoshi
authors.initials: S
authors.lastname: Oota
authors.forename: Wojciech
authors.initials: W
authors.lastname: Makalowski
authors.forename: Kazuho
authors.initials: K
authors.lastname: Ikeo
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Kousuke
authors.initials: K
authors.lastname: Hanada
authors.forename: Katsuyuki
authors.initials: K
authors.lastname: Hashimoto
authors.forename: Momoki
authors.initials: M
authors.lastname: Hirai
authors.forename: Hisakazu
authors.initials: H
authors.lastname: Iwama
authors.forename: Naruya
authors.initials: N
authors.lastname: Saitou
authors.forename: Aiko T
authors.initials: AT
authors.lastname: Hiraki
authors.forename: Lihua
authors.initials: L
authors.lastname: Jin
authors.forename: Yayoi
authors.initials: Y
authors.lastname: Kaneko
authors.forename: Masako
authors.initials: M
authors.lastname: Kanno
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Murakami
authors.forename: Akiko Ogura
authors.initials: AO
authors.lastname: Noda
authors.forename: Naomi
authors.initials: N
authors.lastname: Saichi
authors.forename: Ryoko
authors.initials: R
authors.lastname: Sanbonmatsu
authors.forename: Mami
authors.initials: M
authors.lastname: Suzuki
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Takeda
authors.forename: Masayuki
authors.initials: M
authors.lastname: Tanaka
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Tadashi
authors.initials: T
authors.lastname: Imanishi
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D005796:Genes; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D020407:Internet; D010802:Phylogeny; D012333:RNA, Messenger / Q000737:chemistry; D012641:Selection, Genetic; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D026801:Synteny
chemical_list: D012333:RNA, Messenger