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, 36 (Database issue), D787-92

Evola: Ortholog Database of All Human Genes in H-InvDB With Manual Curation of Phylogenetic Trees

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Evola: Ortholog Database of All Human Genes in H-InvDB With Manual Curation of Phylogenetic Trees

Akihiro Matsuya et al. Nucleic Acids Res.

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 '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/.

Figures

Figure 1.
Figure 1.
An example of manually curated gene pair from H.sapiens (red underline) and Macaca.sp (blue underline). In this case, conditions of phylogenetic topologies, outgroup species (light gray background) and bootstrap values (two circles) are sufficient (refer to the text). Thus, the pair was defined as a manually curated ortholog.
Figure 2.
Figure 2.
Evola main page. This page is divided into left and right frames. In the left frame, tables of orthologs, download data, Gene ontology, and InterPro are listed. Three green buttons are links to show ‘Alignment’ (A), ‘dN/dS view’ (B) and ‘Locus maps’ (C) in the right frame.

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