DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads.

Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies.

The Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) has operated biological databases since 1987 in collaboration with NCBI and EBI. As one of the three major public databases, CIB-DDBJ has run four primary databases DDBJ, CIBEX, DDBJ Trace Archive (DTA), and DDBJ Read Archive (DRA) to collect, archive, and provide various kinds of biological data. As the massively parallel new sequencing platforms are increasingly in use, huge amounts of the raw data have been produced.

The origin of peroxisomes: The possibility of an actinobacterial symbiosis.

The peroxisome is an organelle found in most eukaryotes that is crucial for lipid metabolism. The ability of peroxisomes to divide themselves and transport post-translational proteins suggests that the peroxisome may have had an endosymbiotic origin. However, the localization of peroxisomal proteins to the endoplasmic reticulum (ER) and the similarity of some peroxisomal proteins to those localized in the ER suggest an alternative hypothesis: that the peroxisome was developed from the ER.

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs.

Here, we constructed a phylogenetic tree of 17 bacterial phyla covering eubacteria and archaea by using a new method and 102 carefully selected orthologs from their genomes. One of the serious disturbing factors in phylogeny construction is the existence of out-paralogs that cannot easily be found out and discarded. In our method, out-paralogs are detected and removed by constructing a phylogenetic tree of the genes in question and examining the clustered genes in the tree.

Comprehensive analysis of the origin of eukaryotic genomes.

There is currently no consensus on the evolutionary origin of eukaryotes. In the search of the ancestors of eukaryotes, we analyzed the phylogeny of 46 genomes, including those of 2 eukaryotes, 8 archaea, and 36 eubacteria. To avoid the effects of gene duplications, we used inparalog pairs of genes with orthologous relationships.

Determination of whole prokaryotic phylogeny by the development of a random extraction method.

The construction of accurate prokaryotic phylogeny is important not only in the field of evolutionary biology, but also in microbiology and pathology. However, in constructing a phylogenetic tree to trace prokaryotic evolution, the phylogenetic relationship is often changed by the choice of species. For the estimation of the accurate lineage of prokaryotes, a new method, named the "random extraction method", was developed.

Association of an intronic polymorphism in the midkine (MK) gene with human sporadic colorectal cancer.

Midkine (MK) is a heparin-binding growth factor specified by a retinoic acid responsive gene. It plays important roles in development and carcinogenesis. The MK gene is located on chromosome 11q11.