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

被引：30

作者：

Matsuya, Akihiro ^{[1
,2
]}

Sakate, Ryuichi ^{[1
]}

Kawahara, Yoshihiro ^{[1
]}

Koyanagi, Kanako O. ^{[3
]}

Sato, Yoshiharu ^{[1
]}

Fujii, Yasuyuki ^{[1
]}

Yamasaki, Chisato ^{[1
]}

Habara, Takuya ^{[1
]}

Nakaoka, Hajime

Todokoro, Fusano ^{[4
]}

Yamaguchi, Kaori ^{[1
]}

Endo, Toshinori ^{[3
]}

Oota, Satoshi ^{[5
]}

Makalowski, Wojciech ^{[6
]}

Ikeo, Kazuho ^{[7
,8
]}

Suzuki, Yoshiyuki ^{[7
,8
]}

Hanada, Kousuke ^{[7
,8
]}

Hashimoto, Katsuyuki ^{[9
]}

Hirai, Momoki ^{[10
]}

Iwama, Hisakazu ^{[11
]}

Saitou, Naruya ^{[12
]}

Hiraki, Aiko T. ^{[1
]}

Jin, Lihua ^{[7
,8
]}

Kaneko, Yayoi ^{[1
]}

Kanno, Masako ^{[1
]}

Murakami, Katsuhiko ^{[1
]}

Noda, Akiko Ogura ^{[1
]}

Saichi, Naomi ^{[1
]}

Sanbonmatsu, Ryoko ^{[1
]}

Suzuki, Mami ^{[1
]}

Takeda, Jun-Ichi ^{[1
]}

Tanaka, Masayuki ^{[1
]}

Gojobori, Takashi ^{[1
,7
,8
]}

Imanishi, Tadashi ^{[1
]}

Itoh, Takeshi ^{[1
,13
]}

机构：

[1] Natl Inst Adv Ind Sci & Technol, Japan Biol Informat Res Ctr, Japan Biol Informat Consrotium, Integrated Database Grp, Tokyo, Japan

[2] Hitachi Co Ltd, Govt & Publ Corp Informat Syst, Tokyo, Japan

[3] Hokkaido Univ, Grad Sch Informat Sci & Technol, Sapporo, Hokkaido 060, Japan

[4] DYNACOM Co Ltd, Chiba, Japan

[5] RIKEN, Bioresource Ctr, Ibaraki, Japan

[6] Univ Munster, Inst Bioinformat, Munster, Germany

[7] Natl Inst Genet, DNA Data Bank Japan, Shizuoka, Japan

[8] Natl Inst Genet, Ctr Informat Biol, Shizuoka, Japan

[9] Natl Inst Biomed Innovat, Dept Biomed Resources, Osaka, Japan

[10] Tokyo Womens Med Univ, Int Res & Educ Inst Integrated Med Sci, Tokyo, Japan

[11] Kagawa Univ, Kagawa, Japan

[12] Natl Inst Genet, Dept Populat Genet, Shizuoka, Japan

[13] Natl Inst Agrobiol Sci, Div Genome & Biodivers Res, Ibaraki, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkm878

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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/.

引用

页码：D787 / D792

页数：6

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