G-compass: a web-based comparative genome browser between human and other vertebrate genomes

Summary: G-compass is designed for efficient comparative genome analysis between human and other vertebrate genomes. The current version of G-compass allows us to browse two corresponding genomic regions between human and another species in parallel. One-to-one evolutionarily conserved regions (i.e. orthologous regions) between species are highlighted along the genomes. Information such as locations of duplicated regions, copy number variations and mammalian ultra-conserved elements is also provided. These features of G-compass enable us to easily determine patterns of genomic rearrangements and changes in gene orders through evolutionary time. Since G-compass is a satellite database of H-InvDB, which is a comprehensive annotation resource for human genes and transcripts, users can easily refer to manually curated functional annotations and other abundant biological information for each human transcript. G-compass is expected to be a valuable tool for comparing human and model organisms and promoting the exchange of functional information

H-InvDB in 2009: extended database and data mining resources for human genes and transcripts

We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219 765 human transcripts in 43 159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources—‘Navigation search’, ‘H-InvDB Enrichment Analysis Tool (HEAT)’ and web service APIs. ‘Navigation search’ is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Social object play between captive bottlenose and Risso's dolphins

<div><p>Many animal species engage in social object play with movable objects. Two bottlenose dolphins (<i>Tursiops truncatus</i>) and one Risso’s dolphin (<i>Grampus griseus</i>) owned by the Kujukushima Aquarium, Japan, occasionally shared and played with an object. Herein, we report social object play between two dolphins exchanging a ball in water. Just before delivery of the ball, one dolphin made an action to request the ball from the dolphin that possessed the ball. This request behavior is also discussed in this report. This study is the first to report two different cetacean species engaging in social object play with one object.</p></div

Ball exchange between a bottlenose dolphin (Niha) and a Risso’s dolphin (Lily).

<p>Lily released the ball from her mouth and Niha caught it.</p

An example of a bout of social object play.

<p>The vertical axis indicates the individual, and the horizontal axis indicates time. The hatched bar is the time of possession of the ball. The arrow indicates the destination of the ball. In this figure, Nami (bottlenose dolphin) possesses the ball by herself, whereas Niha (bottlenose dolphin) and Lily (Risso’s dolphin) share the ball.</p

Data from Social object play between captive bottlenose and Risso’s dolphins

<p>The file set contains video and excel data of social object play between captive bottlenose and Risso's dolphins taken at the Kujukushima Aquarium, Umi Kirara, Japan.</p

H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts

H-Invitational Database (H-InvDB; &#x22;http://www.h-invitational.jp/&#x22;:http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. The latest release of H-InvDB (release 6.0) provide annotation for 219,765 human transcripts in 43,159 human gene clusters based on human FLcDNAs and mRNAs.&#xd;&#xa;&#xd;&#xa;H-InvDB consists of two main views, the Transcript view and the Locus view, and six auxiliary databases with web-based viewers; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view. We also provides several data mining tools such as &#xd;&#xa;&#x201c;Navi search&#x201d;: consists of 16 search contents each of which includes items for the search condition (&#x22;http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp&#x22;:http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp), &#x201c;PANDA&#x201d;: Priority ANalysis for Disease Association (PANDA) system (&#x22;http://www.h-invitational.jp/panda/app&#x22;:http://www.h-invitational.jp/panda/app), H-InvDB now provides web service APIs of SOAP and REST to use H-InvDB data in programs. (&#x22;http://www.h-invitational.jp/hinv/hws/doc/&#x22;:http://www.h-invitational.jp/hinv/hws/doc/)&#xd;&#xa;&#xd;&#xa