Takehide Kosuge

Publications of Takehide Kosuge

• DDBJ progress report.

  Authors: Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura

  Nucleic acids research. 11/2010; 39(Database issue):D22-7.

  The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotationThe DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. The DDBJ collected and released 3,637,446 entries/2,272,231,889 bases between July 2009 and June 2010. A highlight of the released data was archive datasets from next-generation sequencing reads of Japanese rice cultivar, Koshihikari submitted by the National Institute of Agrobiological Sciences. In this period, we started a new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline. In this article, we describe these new functions of the DDBJ databases and support tools.

• Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).

  Authors: Takehide Kosuge, Takashi Abe, Toshihisa Okido, Naoto Tanaka, Masaki Hirahata, Yutaka Maruyama, Jun Mashima, Aki Tomiki, Motoyoshi Kurokawa, Ryutaro Himeno, Satoshi Fukuchi, Satoru Miyazaki, Takashi Gojobori, Yoshio Tateno, Hideaki Sugawara

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2007; 13(6):245-54.

  A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB,A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ac.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.

• Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.

  Authors: Monica Riley, Takashi Abe, Martha B Arnaud, Mary K B Berlyn, Frederick R Blattner, Roy R Chaudhuri, Jeremy D Glasner, Takashi Horiuchi, Ingrid M Keseler, Takehide Kosuge, Hirotada Mori, Nicole T Perna, Guy Plunkett, Kenneth E Rudd, Margrethe H Serres, Gavin H Thomas, Nicholas R Thomson, David Wishart, Barry L Wanner

  Nucleic acids research. 02/2006; 34(1):1-9.

  The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes,The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.

• Evidence standards in experimental and inferential INSDC Third Party Annotation data.

  Authors: Guy Cochrane, Kirsty Bates, Rolf Apweiler, Yoshio Tateno, Jun Mashima, Takehide Kosuge, Ilene Karsch-Mizrachi, Susan Schafer, Michael Fetchko

  Omics : a journal of integrative biology. 02/2006; 10(2):105-13.

  The Third Party Annotation (TPA) project collects and presents high-quality annotation of nucleotide sequence. Annotation is submitted by researchers who have not themselves generated novelThe Third Party Annotation (TPA) project collects and presents high-quality annotation of nucleotide sequence. Annotation is submitted by researchers who have not themselves generated novel nucleotide sequence. In its first few years, the resource has proven to be popular with submitters from a range of biological research areas. Central to the project is the requirement for high-quality data, resulting from experimental and inferred analysis discussed in peer-reviewed publications. The data are divided into two tiers: those with experimental evidence and those with inferential evidence. Standards for TPA are detailed and illustrated with the aid of case studies.

• DDBJ Activities: Contribution to the Research in Information Biology

  Authors: Jun Mashima, Takehide Kosuge, Toshihisa Okido, Yuichi Kodama, Kazuho Ikeo, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori

  Nature Precedings.

  DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International NucleotideDDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also collecting and releasing gene expression data at CIBEX (Center for Information Biology gene EXpression database; "http://cibex.nig.ac.jp/":http://cibex.nig.ac.jp/). Furthermore, DDBJ contributed to international annotation jamborees such as FANTOM (mouse), H-Inv (human), RAP (rice) and E. coli K12. DDBJ provides many services to the research in information biology or bioinformatics. They include Web-API for Biology (WABI) "http://www.xml.nig.ac.jp/":http://www.xml.nig.ac.jp/ and All-round Retrieval of Sequence and Annotation (ARSA) "http://arsa.ddbj.nig.ac.jp/":http://arsa.ddbj.nig.ac.jp/. These activities are presented with the perspective of DDBJ in the coming years.