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

Akihiro Matsuya; Ryuichi Sakate; Yoshihiro Kawahara; Kanako O. Koyanagi; Yoshiharu Sato; Yasuyuki Fujii; Chisato Yamasaki; Takuya Habara; Hajime Nakaoka; Fusano Todokoro; Kaori Yamaguchi; Toshinori Endo; Satoshi Oota; Wojciech Makalowski; Kazuho Ikeo; Yoshiyuki Suzuki; Kousuke Hanada; Katsuyuki Hashimoto; Momoki Hirai; Hisakazu Iwama; Naruya Saitou; Aiko T. Hiraki; Lihua Jin; Yayoi Kaneko; Masako Kanno; Katsuhiko Murakami; Akiko Ogura Noda; Naomi Saichi; Ryoko Sanbonmatsu; Mami Suzuki; Jun-Ichi Takeda; Masayuki Tanaka; Takashi Gojobori; Tadashi Imanishi; Takeshi Itoh

doi:10.1093/nar/gkm878

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

Journal article

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

Akihiro Matsuya, Ryuichi Sakate, Yoshihiro Kawahara, Kanako O. Koyanagi, Yoshiharu Sato, Yasuyuki Fujii, Chisato Yamasaki, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, …

Nucleic acids research, Vol.36(suppl-1), pp.D787-D792

01/01/2008

DOI: https://doi.org/10.1093/nar/gkm878

PMCID: PMC2238928

PMID: 17982176

Abstract

Biochemistry & Molecular Biology

Life Sciences & Biomedicine

Science & Technology

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/.

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Title: Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Creators - without role: Akihiro Matsuya - Japan Biological Informatics Consortium
Ryuichi Sakate - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Yoshihiro Kawahara - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Kanako O. Koyanagi - Hokkaido University
Yoshiharu Sato - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Yasuyuki Fujii - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Chisato Yamasaki - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Takuya Habara - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Hajime Nakaoka
Fusano Todokoro - DYNACOM Co Ltd, Chiba, Japan
Kaori Yamaguchi - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Toshinori Endo - Hokkaido University
Satoshi Oota - RIKEN
Wojciech Makalowski - University of Münster
Kazuho Ikeo - Bank of Japan
Yoshiyuki Suzuki - Bank of Japan
Kousuke Hanada - Bank of Japan
Katsuyuki Hashimoto - Natl Inst Biomed Innovat, Dept Biomed Resources, Osaka, Japan
Momoki Hirai - College Station Medical Center
Hisakazu Iwama - Kagawa University
Naruya Saitou - Natl Inst Genet, Dept Populat Genet, Shizuoka, Japan
Aiko T. Hiraki - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Lihua Jin - Bank of Japan
Yayoi Kaneko - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Masako Kanno - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Katsuhiko Murakami - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Akiko Ogura Noda - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Naomi Saichi - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Ryoko Sanbonmatsu - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Mami Suzuki - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Jun-Ichi Takeda - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Masayuki Tanaka - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Takashi Gojobori - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Tadashi Imanishi - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Takeshi Itoh - Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan
Publication Details: Nucleic acids research, Vol.36(suppl-1), pp.D787-D792
Publisher: Oxford Univ Press
Number of pages: 6
Identifiers: 9942926708331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article