| 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)
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