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

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Please use this identifier to cite or link to this item:http://hdl.handle.net/2115/50048

Title: Evola : Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Authors: Matsuya, Akihiro Browse this author
Sakate, Ryuichi Browse this author
Kawahara, Yoshihiro Browse this author
Koyanagi, Kanako O. Browse this author
Sato, Yoshiharu Browse this author
Fujii, Yasuyuki Browse this author
Yamasaki, Chisato Browse this author
Habara, Takuya Browse this author
Nakaoka, Hajime Browse this author
Todokoro, Fusano Browse this author
Yamaguchi, Kaori Browse this author
Endo, Toshinori Browse this author
OOta, Satoshi Browse this author
Makalowski, Wojciech Browse this author
Ikeo, Kazuho Browse this author
Suzuki, Yoshiyuki Browse this author
Hanada, Kousuke Browse this author
Hashimoto, Katsuyuki Browse this author
Hirai, Momoki Browse this author
Iwama, Hisakazu Browse this author
Saitou, Naruya Browse this author
Hiraki, Aiko T. Browse this author
Jin, Lihua Browse this author
Kaneko, Yayoi Browse this author
Kanno, Masako Browse this author
Murakami, Katsuhiko Browse this author
Noda, Akiko Ogura Browse this author
Saichi, Naomi Browse this author
Sanbonmatsu, Ryoko Browse this author
Suzuki, Mami Browse this author
Takeda, Jun-ichi Browse this author
Tanaka, Masayuki Browse this author
Gojobori, Takashi Browse this author
Imanishi, Tadashi Browse this author
Itoh, Takeshi Browse this author
Issue Date: Jan-2008
Publisher: Oxford University Press
Journal Title: Nucleic Acids Research
Volume: 36
Issue: supple. 1
Start Page: D787
End Page: D792
Publisher DOI: 10.1093/nar/gkm878
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 ‘dN/dS 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/.
Type: article
URI: http://hdl.handle.net/2115/50048
Appears in Collections:情報科学院・情報科学研究院 (Graduate School of Information Science and Technology / Faculty of Information Science and Technology) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 遠藤 俊徳

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