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Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees

2007; Oxford University Press; Volume: 36; Issue: Database Linguagem: Inglês

10.1093/nar/gkm878

1362-4962

Ayako Matsuya, Ryuichi Sakate, Yoshihiro Kawahara, Kanako O. Koyanagi, Yoshiharu Sato, Yasuyuki Fujii, Chihiro Yamasaki, Toshiaki Habara, Hirofumi Nakaoka, Fusano Todokoro, Koji Yamaguchi, Toshio Endo, Satoshi Oota, Wojciech Makałowski, Kazuho Ikeo, Y. Suzuki, Kousuke Hanada, Katsuyuki Hashimoto, Momoki Hirai, Hisakazu Iwama, Naruya Saitou, Aiko T. Hiraki, Lijun Jin, Yayoi Kaneko, Masamoto Kanno, Katsuhiko Murakami, Akiko Noda, Naomi Saichi, Ryoko Sanbonmatsu, Mami Suzuki, Jun‐ichi Takeda, Masayuki Tanaka, Takashi Gojobori, Tadashi Imanishi, Takeshi Itoh,

Machine Learning in Bioinformatics

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/ .